name: regulation of opsin-mediated signaling pathway

description: Any process that modulates the frequency, rate or extent of opsin-mediated signaling.


name: regulatory ncRNA-mediated post-transcriptional gene silencing

category: biolink:BiologicalProcess biolink:Occurrent biolink:OntologyClass biolink:BiologicalProcessOrActivity biolink:BiologicalEntity biolink:ThingWithTaxon biolink:NamedThing biolink:PhysicalEssenceOrOccurrent

description: A posttranscriptional gene silencing pathway in which regulatory RNAs elicit silencing of specific target genes, either by mRNA destabilization or inhibition of translation.


siRNA processing

description: A process leading to the generation of a functional small interfering RNA (siRNA). Includes the cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides. May also include amplification of the siRNA by RNA-directed RNA polymerase.


name: regulation of keratinocyte differentiation

description: Any process that modulates the frequency, rate or extent of keratinocyte differentiation.


carboxylic acid metabolic process

description: The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).


name: protein N-linked glycosylation via asparagine

description: The glycosylation of protein via the N4 atom of peptidyl-asparagine forming N4-glycosyl-L-asparagine; the most common form is N-acetylglucosaminyl asparagine; N-acetylgalactosaminyl asparagine and N4 glucosyl asparagine also occur. This modification typically occurs in extracellular peptides with an N-X-(ST) motif. Partial modification has been observed to occur with cysteine, rather than serine or threonine, in the third position; secondary structure features are important, and proline in the second or fourth positions inhibits modification.


name: positive regulation of neurotrophin TRK receptor signaling pathway

description: Any process that activates or increases the frequency, rate or extent of the neurotrophin TRK receptor signaling pathway.


vitamin D metabolic process

description: The chemical reactions and pathways involving vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3).


category: biolink:Pathway biolink:OntologyClass biolink:BiologicalProcess biolink:Occurrent biolink:BiologicalProcessOrActivity biolink:BiologicalEntity biolink:ThingWithTaxon biolink:NamedThing biolink:PhysicalEssenceOrOccurrent

description: The series of molecular signals initiated by interleukin-23 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


response to metal ion

description: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a metal ion stimulus.


name: transcription initiation at mitochondrial promoter

description: A transcription initiation process that takes place at a promoter on the mitochondrial chromosome.


glucocorticoid biosynthetic process

description: The chemical reactions and pathways resulting in the formation of glucocorticoids, hormonal C21 corticosteroids synthesized from cholesterol.


name: C21-steroid hormone biosynthetic process

description: The chemical reactions and pathways resulting in the formation of C21-steroid hormones, steroid compounds containing 21 carbons which function as hormones.


folic acid metabolic process

description: The chemical reactions and pathways involving folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.


gap junction assembly

description: Assembly of gap junctions, which are found in most animal tissues, and serve as direct connections between the cytoplasms of adjacent cells. They provide open channels through the plasma membrane, allowing ions and small molecules (less than approximately a thousand daltons) to diffuse freely between neighboring cells, but preventing the passage of proteins and nucleic acids.


name: positive regulation of receptor signaling pathway via STAT

description: Any process that activates or increases the frequency, rate or extent of receptor signaling pathway via STAT.


name: regulation of megakaryocyte differentiation

description: Any process that modulates the frequency, rate or extent of megakaryocyte differentiation.


DNA alkylation repair

description: The repair of alkylation damage in DNA, e.g. the removal of a non-physiological alkyl group from a nucleobase. This is usually mediated by DNA alkyltransferases.


name: death-inducing signaling complex assembly

description: A process of protein complex assembly in which the arrangement and bonding together of the set of components that form the protein complex is mediated by a death domain (DD) interaction, as part of the extrinsic apoptotic signaling pathway.


name: activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway

description: Any process that initiates the activity of an inactive cysteine-type endopeptidase involved in the apoptotic signaling pathway.


depurination

description: The disruption of the bond between the sugar in the backbone and the A or G base, causing the base to be removed and leaving a depurinated sugar.


depyrimidination

description: The disruption of the bond between the sugar in the backbone and the C or T base, causing the base to be removed and leaving a depyrimidinated sugar.


histone mRNA metabolic process

description: The chemical reactions and pathways involving an mRNA encoding a histone.


base-excision repair, DNA ligation

description: The ligation by DNA ligase of DNA strands. Ligation occurs after polymerase action to fill the gap left by the action of endonucleases during base-excision repair.


intracellular transport of virus

description: The directed movement of a virus, or part of a virus, within the host cell.


ERBB2 signaling pathway

description: The series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor ERBB2 on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB2 receptors are themselves unable to bind to ligands, but act as a signal-amplifying tyrosine kinase within a heterodimeric pair.


name: antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent

description: The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a pathway not requiring TAP (transporter associated with antigen processing). The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell. Class I here refers to classical class I molecules.


name: vesicle fusion with endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane

description: The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane of the ERGIC. This can involve anterograde or retrograde transport vesicles.


name: negative regulation of blood coagulation, extrinsic pathway

description: Any process that stops, prevents or reduces the frequency, rate or extent of blood coagulation, extrinsic pathway.


name: negative regulation of blood coagulation, intrinsic pathway

description: Any process that stops, prevents or reduces the frequency, rate or extent of blood coagulation, intrinsic pathway.


inositol phosphate metabolic process

description: The chemical reactions and pathways involving inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached.


C-terminal protein lipidation

description: The covalent attachment of a lipid group to the carboxy-terminus of a protein.


sulfur amino acid catabolic process

description: The chemical reactions and pathways resulting in the breakdown of amino acids containing sulfur, comprising cysteine, methionine and selenocysteine.


sulfur amino acid metabolic process

description: The chemical reactions and pathways involving amino acids containing sulfur, comprising cysteine, homocysteine, methionine and selenocysteine.


name: termination of mitochondrial transcription

description: A transcription termination process that completes the production of a primary mitochondrial transcript.


activation of protein kinase A activity

description: Any process that initiates the activity of the inactive enzyme protein kinase A.


name: positive regulation of cellular metabolic process

description: Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.


name: negative regulation of MyD88-independent toll-like receptor signaling pathway

description: Any process that stops, prevents, or reduces the frequency, rate, or extent of MyD88-independent toll-like receptor signaling pathway.


toll-like receptor 10 signaling pathway

description: The series of molecular signals initiated by a ligand binding to toll-like receptor 10.


name: toll-like receptor TLR1:TLR2 signaling pathway

description: The series of molecular signals initiated by a ligand binding of a heterodimeric TLR1:TLR2 complex, followed by transmission of the signal by the activated receptor, and ending with the regulation of a downstream cellular process, e.g. transcription.


name: telomere maintenance via semi-conservative replication

description: The process in which telomeric DNA is synthesized semi-conservatively by the conventional replication machinery and telomeric accessory factors as part of cell cycle DNA replication.


name: regulation of anaphase-promoting complex-dependent catabolic process

description: Any process that modulates the frequency, rate or extent of anaphase-promoting complex-dependent catabolic process.


name: negative regulation of ERBB signaling pathway

description: Any process that stops, prevents or reduces the frequency, rate or extent of ERBB signaling pathway.


name: negative regulation of platelet-derived growth factor receptor-beta signaling pathway

description: Any process that stops, prevents or reduces the frequency, rate or extent of platelet-derived growth factor receptor-beta signaling pathway.


import into nucleus

description: The directed movement of substances into the nucleus.


spliceosomal snRNP assembly

description: The aggregation, arrangement and bonding together of one or more snRNA and multiple protein components to form a ribonucleoprotein complex that is involved in formation of the spliceosome.


name: beta-catenin destruction complex assembly

description: The aggregation, arrangement and bonding together of a set of components to form a beta-catenin destruction complex.


carnitine shuttle

description: The transfer of acyl groups to and from acyl-CoA molecules to form O-acylcarnitine, which can exchange across the mitochondrial inner membrane with unacylated carnitine.


name: sequestering of BMP from receptor via BMP binding

description: Binding to a bone morphogenetic protein (BMP) in the extracellular region, and inhibiting BMP signaling by preventing BMP from binding to its cell surface receptor.


name: regulation of transcription initiation by RNA polymerase II

description: Any process that modulates the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter.


ferredoxin metabolic process

description: The chemical reactions and pathways involving ferredoxin, any simple, nonenzymatic iron-sulfur protein that is characterized by having equal numbers of atoms of iron and labile sulfur. Iron and sulfur atoms are present in one or two clusters of two or four atoms of each.


selenocysteine metabolic process

description: The chemical reactions and pathways involving selenocysteine, an essential component of glutathione peroxidase and some other proteins.


Fc-epsilon receptor signaling pathway

description: The series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.


name: regulation of extrinsic apoptotic signaling pathway via death domain receptors

description: Any process that modulates the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.


name: negative regulation of netrin-activated signaling pathway

description: Any process that stops, prevents or reduces the frequency, rate or extent of netrin-activated signaling pathway.


name: chaperone mediated protein folding independent of cofactor

description: The process of assisting in the correct noncovalent assembly of posttranslational proteins and does not depend on additional protein cofactors. This function occurs over one or more cycles of nucleotide-dependent binding and release.


post-chaperonin tubulin folding pathway

description: Completion of folding of alpha- and beta-tubulin; takes place subsequent to chaperonin-mediated partial folding; mediated by a complex of folding cofactors.


muscle filament sliding

description: The sliding of actin thin filaments and myosin thick filaments past each other in muscle contraction. This involves a process of interaction of myosin located on a thick filament with actin located on a thin filament. During this process ATP is split and forces are generated.


hemidesmosome assembly

description: Assembly of hemidesmosomes, integrin-containing protein complexes that bind to laminin in the basal lamina. Hemidesmosomes form the contact between the basal surface of epithelial cells and the underlying basal lamina.


mitochondrial translational termination

description: The process resulting in the release of a polypeptide chain from the ribosome in a mitochondrion, usually in response to a termination codon (note that mitochondria use variants of the universal genetic code that differ between different taxa).


aflatoxin metabolic process

description: The chemical reactions and pathways involving aflatoxin, a fungal metabolite found as a contaminant in moldy grains that induces liver cancer. Aflatoxin induces a G to T transversion at codon 249 of p53, leading to its inactivation. Aflatoxin is converted to a chemical carcinogen by P450.


piRNA processing

description: A process leading to the generation of a functional piRNA. piRNAs (Piwi-associated RNAs) are a class of 24- to 30-nucleotide RNAs derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism.


name: intraciliary transport involved in cilium assembly

description: The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly.


DNA synthesis involved in DNA repair

description: Synthesis of DNA that proceeds from the broken 3' single-strand DNA end and uses the homologous intact duplex as the template.


DNA strand displacement

description: The rejection of the broken 3' single-strand DNA molecule that formed heteroduplex DNA with its complement in an intact duplex DNA. The Watson-Crick base pairing in the original duplex is restored. The rejected 3' single-strand DNA molecule reanneals with its original complement to reform two intact duplex molecules.


name: nucleotide-excision repair, DNA damage recognition

description: The identification of lesions in DNA, such as pyrimidine-dimers, intrastrand cross-links, and bulky adducts. The wide range of substrate specificity suggests the repair complex recognizes distortions in the DNA helix.


name: nucleotide-excision repair, preincision complex stabilization

description: The stabilization of the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage as well as the unwound DNA. The stabilization of the protein-DNA complex ensures proper positioning of the preincision complex before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.


name: nucleotide-excision repair, DNA duplex unwinding

description: The unwinding, or local denaturation, of the DNA duplex to create a bubble around the site of the DNA damage.


name: nucleotide-excision repair, DNA gap filling

description: Repair of the gap in the DNA helix by DNA polymerase and DNA ligase after the portion of the strand containing the lesion has been removed by pyrimidine-dimer repair enzymes.


glycine catabolic process

description: The chemical reactions and pathways resulting in the breakdown of glycine, aminoethanoic acid.


name: negative regulation of cellular amino acid metabolic process

description: Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid.


name: positive regulation of amino acid metabolic process

description: Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amino acid.


name: purine ribonucleoside monophosphate biosynthetic process

description: The chemical reactions and pathways resulting in the formation of purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar.


name: regulation of cell cycle G2/M phase transition

description: Any signaling pathway that modulates the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the cell cycle.


SCF complex assembly

description: The aggregation, arrangement and bonding together of a set of components to form the SKP1-Cullin/Cdc53-F-box protein ubiquitin ligase (SCF) complex.


name: low-density lipoprotein particle receptor catabolic process

description: The chemical reactions and pathways resulting in the breakdown of a low-density lipoprotein particle receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.


digestion

description: The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.


name: regulation of B cell receptor signaling pathway

description: Any process that modulates the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a B cell.


name: regulation of cytokine-mediated signaling pathway

description: Any process that modulates the frequency, rate or extent of the cytokine mediated signaling pathway.


protein side chain deglutamylation

description: The removal of a glutamate residue from the side chain of a protein. Glutamate side chains are added to glutamic acid residues within the primary protein sequence during polyglutamylation.


protein polyglycylation

description: The addition of glycyl units covalently bound to the gamma carboxyl group peptidyl-glutamic acid.


name: C-terminal protein amino acid modification

description: The alteration of the C-terminal amino acid residue in a protein.


chylomicron remodeling

description: The acquisition, loss or modification of a protein or lipid within a chylomicron, including the hydrolysis of triglyceride by lipoprotein lipase and the subsequent loss of free fatty acid.


name: high-density lipoprotein particle clearance

description: The process in which a high-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.


name: very-low-density lipoprotein particle clearance

description: The process in which a very-low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.


name: high-density lipoprotein particle remodeling

description: The acquisition, loss or modification of a protein or lipid within a high-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters from LDL to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride to LDL.


description: The series of molecular signals initiated by erythropoietin (EPO) binding to the erythropoietin receptor (EPO-R) on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


description: The series of molecular signals initiated by interleukin-35 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


name: negative regulation of primary miRNA processing

description: Any process that stops, prevents or reduces the frequency, rate or extent of primary microRNA processing.


trimming of first mannose on A branch

description: The removal of the first alpha-1,2-linked mannose from the A-chain of a glycoprotein oligosaccharide in the endoplasmic reticulum.


name: trimming of terminal mannose on B branch

description: The removal of an alpha-1,2-linked mannose from the B-chain of a glycoprotein oligosaccharide in the endoplasmic reticulum.


name: mannose trimming involved in glycoprotein ERAD pathway

description: The removal of one or more alpha 1,2-linked mannose residues from a mannosylated protein that occurs as part of glycoprotein ER-associated glycoprotein degradation (gpERAD).


trimming of second mannose on A branch

description: The removal of the second alpha-1,2-linked mannose from the A-chain of a glycoprotein oligosaccharide in the endoplasmic reticulum.


name: trimming of terminal mannose on C branch

description: The removal of an alpha-1,2-linked mannose from the C-chain of a glycoprotein oligosaccharide in the endoplasmic reticulum.


endoplasmic reticulum mannose trimming

description: Any protein alpha-1,2-demannosylation that takes place in the endoplasmic reticulum quality control compartment (ERQC).


name: Notch receptor processing, ligand-dependent

description: The proteolytic cleavages to the Notch protein that occur as a result of ligand binding. Ligand binding at the cell surface exposes an otherwise inaccessible cleavage site in the extracellular portion of Notch, which when cleaved releases a membrane-tethered form of the Notch intracellular domain. Subsequent cleavage within the transmembrane domain then leads to the release of the soluble Notch intracellular domain (NICD).


description: The series of molecular signals initiated by interleukin-27 binding to a receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


description: The series of molecular signals initiated by interleukin-21 binding to a receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


protein import into peroxisome membrane

description: The targeting of proteins into the peroxisomal membrane. The process is not well understood, but both signals and mechanism differ from those involved in peroxisomal matrix protein import.


protein insertion into ER membrane

description: The process that results in incorporation of a protein into an endoplasmic reticulum (ER) membrane. It depends on specific topogenic sequences of amino acids that ensure that a protein acquires the proper orientation during its insertion into the ER membrane.


late endosomal microautophagy

description: The autophagy process by which cytosolic proteins targeted for degradation are tagged with a chaperone and are directly transferred into and degraded in a late endosomal compartment.


regulation of heme oxygenase activity

description: Any process that modulates the frequency, or rate of heme oxygenase activity.


lateral mesoderm formation

description: The process that gives rise to the lateral mesoderm. This process pertains to the initial formation of the structure from unspecified parts.


name: growth hormone receptor signaling pathway via JAK-STAT

description: The process in which STAT proteins (Signal Transducers and Activators of Transcription) are activated by members of the JAK (janus activated kinase) family of tyrosine kinases, following the binding of physiological ligands to the growth hormone receptor. Once activated, STATs dimerize and translocate to the nucleus and modulate the expression of target genes.


name: TFAM_HUMAN Transcription factor A, mitochondrial (sprot)

description: A transcription factor A, mitochondrial that is encoded in the genome of human.


phosphatidylinositol 3-phosphate

A phosphatidylinositol monophosphate carrying the phosphate group at the 3-position.


name: NDST1_HUMAN Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 (sprot)

description: A bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 that is encoded in the genome of human.


A C4-dicarboxylate that is the E-isomer of but-2-enedioate(2-)


An optically active form of malate having (S)-configuration.


A C4-dicarboxylate resuting from deprotonation of both carboxy groups of oxaloacetic acid.


name: SOCS1_HUMAN Suppressor of cytokine signaling 1 (sprot)

description: A suppressor of cytokine signaling 1 that is encoded in the genome of human.


adenosine

A ribonucleoside composed of a molecule of adenine attached to a ribofuranose moiety via a beta-N(9)-glycosidic bond.


DEOXYGUANOSINE

A purine 2'-deoxyribonucleoside having guanine as the nucleobase.


guanosine

A purine nucleoside in which guanine is attached to ribofuranose via a beta-N(9)-glycosidic bond.


inosine

A purine nucleoside in which hypoxanthine is attached to ribofuranose via a beta-N(9)-glycosidic bond.


A purine 2'-deoxyribonucleoside that is inosine in which the hydroxy group at position 2' is replaced by a hydrogen.


uracil

A common and naturally occurring pyrimidine nucleobase in which the pyrimidine ring is substituted with two oxo groups at positions 2 and 4. Found in RNA, it base pairs with adenine and replaces thymine during DNA transcription.


A pyrimidine obtained by formal addition of hydrogen across the 5,6-position of uracil.


A pyrimidone obtained by formal addition of hydrogen across the 5,6-position of thymine.


A 17alpha-hydroxy steroid that is the 17alpha-hydroxy derivative of progesterone.


A deoxycortisol that is cortisol in which the hydroxy group at position 11 has been replaced by a hydrogen.


ceramide

Ceramides (N-acyl-sphingoid bases) are a major subclass of sphingoid base derivatives with an amide-linked fatty acid. The fatty acids are typically saturated or monounsaturated with chain lengths from 14 to 26 carbon atoms; the presence of a hydroxyl group on carbon 2 is fairly common. Ceramides are generally precursors of more complex sphingolipids. In the illustrated generalised structure, R(1) = OH, OX (where X = acyl, glycosyl, phosphate, phosphonate, etc.), or H.


STX17_HUMAN Syntaxin-17 (sprot)

A syntaxin-17 that is encoded in the genome of human.


hypoxanthine

A purine nucleobase that consists of purine bearing an oxo substituent at position 6.


2'-deoxyadenosine 5'-monophosphate(2-)

A 2'-deoxyribonucleoside 5'-monophosphate(2-) obtained by deprotonation of the phosphate OH groups of 2'-deoxyadenosine 5'-monophosphate (dAMP).


2'-deoxyguanosine 5'-monophosphate(2-)

A 2'-deoxyribonucleoside 5'-monophosphate(2-) obtained by deprotonation of the phosphate OH groups of 2'-deoxyguanosine 5'-monophosphate (dGMP).


Dianion of N-phosphocreatine arising from deprotonation of the phospho and carboxy groups and protonation of the guanidino group; major species at pH 7.3.


creatine

A glycine derivative having methyl and amidino groups attached to the nitrogen.


2'-deoxyinosine 5'-phosphate(2-)

A 2'-deoxyribonucleoside 5'-monophosphate(2-) obtained by deprotonation of the phosphate OH groups of 2'-deoxyinosine 5'-monophosphate; major species at pH 7.3.


A 2'-deoxyribonucleoside 5'-triphosphate(4-) resulting from deprotonation of the triphosphate OH groups of 2'-deoxyuridine-5'-triphosphate (dUTP); major species at pH 7.3.


A nucleoside 5'-diphosphate(3-) arising from deprotonation of the diphosphate OH groups of uridine 5'-diphosphate (UDP); major species at pH 7.3.


A 2'-deoxyribonucleoside 5'-diphosphate obtained by deprotonation of the diphosphate OH groups of 2'-deoxyuridine 5'-diphosphate (dUDP).


L-tryptophan

The L-enantiomer of tryptophan.


SYUA_HUMAN Alpha-synuclein (sprot)

An alpha-synuclein that is encoded in the genome of human.


name: LPIN1_HUMAN Phosphatidate phosphatase LPIN1 (sprot)

description: A phosphatidate phosphatase LPIN1 that is encoded in the genome of human.


name: HDAC3_HUMAN Histone deacetylase 3 (sprot)

description: A histone deacetylase 3 that is encoded in the genome of human.


name: UIMC1_HUMAN BRCA1-A complex subunit RAP80 (sprot)

description: A BRCA1-A complex subunit RAP80 that is encoded in the genome of human.


name: FZR1_HUMAN Fizzy-related protein homolog (sprot)

description: A fizzy-related protein that is encoded in the genome of human.


name: CDK4_HUMAN Cyclin-dependent kinase 4 (sprot)

description: A cell division protein kinase 4 that is encoded in the genome of human.


name: CDK6_HUMAN Cyclin-dependent kinase 6 (sprot)

description: A cyclin-dependent kinase 6 that is encoded in the genome of human.


name: NEDD8 ultimate buster 1 isoform h2 (human)

description: A NEDD8 ultimate buster 1 (human) that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:Q9Y5A7-2.


(R)-mevalonate

The (R)-enantiomer of mevalonate.


A 3-oxo-5alpha- steroid that is zymosterol which has been substituted by a methyl group at C-4, and in which the 3-hydroxy function has been oxidised to an oxo group.


A 3beta-sterol formed formally by loss of a methyl group from the 14-position of lanosterol.


An acyl-CoA oxoanion that results from the removal of all five protons from the phosphate and carboxylic acid groups of (3S)-3-hydroxy-3-methylglutaryl-CoA.


A 2,3-epoxysqualene in which the chiral centre has S configuration. It is converted into lanosterol by lanosterol synthase (EC 5.4.99.7) in a key rate-limiting step in the biosynthesis of chloesterol, steroid hormones, and vitamin D.


lanosterol

A tetracyclic triterpenoid that is lanosta-8,24-diene substituted by a beta-hydroxy group at the 3beta position. It is the compound from which all steroids are derived.


squalene

A triterpene consisting of 2,6,10,15,19,23-hexamethyltetracosane having six double bonds at the 2-, 6-, 10-, 14-, 18- and 22-positions with (all-E)-configuration.


Trianion of (R)-5-phosphomevalonic acid arising from deprotonation of the carboxy and phosphate OH groups; major species at pH 7.3.


A 3-oxoacyl-CoA(4-) arising from deprotonation of the phosphate and diphosphate OH groups of acetoacetyl-CoA.


name: ABCD4_HUMAN Lysosomal cobalamin transporter ABCD4 (sprot)

description: A lysosomal cobalamin transporter ABCD4 that is encoded in the genome of human.


CUBN_HUMAN Cubilin (sprot)

A cubilin that is encoded in the genome of human.


name: G6PT1_HUMAN Glucose-6-phosphate exchanger SLC37A4 (sprot)

description: A glucose-6-phosphate exchanger SLC37A4 that is encoded in the genome of human.


EREG_HUMAN Proepiregulin (sprot)

A proepiregulin that is encoded in the genome of human.


D-galactose

D-Galactopyranose having alpha-configuration at the anomeric centre.


Pentaanion of 5-O-phosphono-alpha-D-ribofuranosyl diphosphate arising from deprotonation of the phosphate and diphosphate OH groups; major species at pH 7.3.


A 2'-deoxyribonucleoside 5'-triphosphate(4-) that is the tetraanion of 2'-deoxyadenosine 5'-triphosphate (dATP), arising from deprotonation of the four triphosphate OH groups; major species at pH 7.3.


The L-enantiomer of argininium(1+).


name: ZDHC9_HUMAN Palmitoyltransferase ZDHHC9 (sprot)

description: A palmitoyltransferase ZDHHC9 that is encoded in the genome of human.


name: CHST7_HUMAN Carbohydrate sulfotransferase 7 (sprot)

description: A carbohydrate sulfotransferase 7 that is encoded in the genome of human.


An NDP-alpha-D-glucose(2-) arising from deprotonation of the diphosphate OH groups of UDP-D-glucose; major species at pH 7.3.


Dianion of UDP-N-acetyl-alpha-D-glucosamine arising from deprotonation of both free diphosphate OH groups; major species at pH 7.3.


name: HS3S5_HUMAN Heparan sulfate glucosamine 3-O-sulfotransferase 5 (sprot)

description: A heparan sulfate glucosamine 3-O-sulfotransferase 5 that is encoded in the genome of human.


name: B4GT1_HUMAN Beta-1,4-galactosyltransferase 1 (sprot)

description: A beta-1,4-galactosyltransferase 1 that is encoded in the genome of human.


name: B3GN7_HUMAN UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7 (sprot)

description: A UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7 that is encoded in the genome of human.


name: B4GA1_HUMAN Beta-1,4-glucuronyltransferase 1 (sprot)

description: A beta-1,4-glucuronyltransferase 1 that is encoded in the genome of human.


name: B3GN3_HUMAN N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 3 (sprot)

description: An N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 3 that is encoded in the genome of human.


name: B3GN4_HUMAN N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 4 (sprot)

description: An N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 4 that is encoded in the genome of human.


name: B3GN2_HUMAN N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2 (sprot)

description: An N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2 that is encoded in the genome of human.


name: CHST1_HUMAN Carbohydrate sulfotransferase 1 (sprot)

description: A carbohydrate sulfotransferase 1 that is encoded in the genome of human.


name: CHD1L_HUMAN Chromodomain-helicase-DNA-binding protein 1-like (sprot)

description: A chromodomain-helicase-DNA-binding protein 1-like that is encoded in the genome of human.


name: DLG4_HUMAN Disks large homolog 4 (sprot)

description: A disks large homolog 4 that is encoded in the genome of human.


glycine

The simplest (and the only achiral) proteinogenic amino acid, with a hydrogen atom as its side chain.


fatty acid anion

The conjugate base of a fatty acid, arising from deprotonation of the carboxylic acid group of the corresponding fatty acid.


The L-enantiomer of 5-hydroxytryptophan.


MUC2_HUMAN Mucin-2 (sprot)

A mucin-2 that is encoded in the genome of human.


TPSN_HUMAN Tapasin (sprot)

A tapasin that is encoded in the genome of human.


chenodeoxycholate

Conjugate base of chenodeoxycholic acid; major species at pH 7.3.


L-ascorbate

The L-enantiomer of ascorbate and conjugate base of L-ascorbic acid, arising from selective deprotonation of the 3-hydroxy group. Required for a range of essential metabolic reactions in all animals and plants.


guanosine 5'-diphosphate

A  purine ribonucleoside 5'-diphosphate resulting from the formal condensation of the hydroxy group at the 5' position of guanosine with pyrophosphoric acid.


name: IFI27_HUMAN Interferon alpha-inducible protein 27, mitochondrial (sprot)

description: An interferon alpha-inducible protein 27 that is encoded in the genome of human.


MUC5B_HUMAN Mucin-5B (sprot)

A mucin-5B that is encoded in the genome of human.


VWF_HUMAN von Willebrand factor (sprot)

A von Willebrand factor that is encoded in the genome of human.


name: GBP2_HUMAN Guanylate-binding protein 2 (sprot)

description: A guanylate-binding protein 2 that is encoded in the genome of human.


name: GBP5_HUMAN Guanylate-binding protein 5 (sprot)

description: A guanylate-binding protein 5 that is encoded in the genome of human.


sulfate

A sulfur oxoanion obtained by deprotonation of both OH groups of sulfuric acid.


alpha-aminoacyl-tRNA

Any ribonucleic acid that is transfer RNA in which one or more of the free OH groups carries an alpha-aminoacyl group.


name: TRNT1_HUMAN CCA tRNA nucleotidyltransferase 1, mitochondrial (sprot)

description: A CCA tRNA nucleotidyltransferase 1, mitochondrial that is encoded in the genome of human.


An organic anion that is the conjugate base of riboflavin resulting from the removal of a proton from the nitrogen at position 3 (between the two carbonyl groups). Major microspecies at pH 7.3.


Trianion of flavin adenine dinucleotide arising from deprotonation of the diphosphate OH groups and the imide nitrogen.


name: A16L1_HUMAN Autophagy-related protein 16-1 (sprot)

description: An autophagy-related protein 16-1 that is encoded in the genome of human.


The conjugate base of a 1-phosphatidyl-1D-myo-inositol; major species at pH 7.3.


name: ATG10_HUMAN Ubiquitin-like-conjugating enzyme ATG10 (sprot)

description: A ubiquitin-like-conjugating enzyme ATG10 that is encoded in the genome of human.


name: ATG12_HUMAN Ubiquitin-like protein ATG12 (sprot)

description: A ubiquitin-like protein ATG12 that is encoded in the genome of human.


ATG5_HUMAN Autophagy protein 5 (sprot)

An autophagy protein 5 that is encoded in the genome of human.


name: HLAA_HUMAN HLA class I histocompatibility antigen, A alpha chain (sprot)

description: An MHC class I histocompatibility antigen A alpha chain that is encoded in the genome of human.


name: PDIA3_HUMAN Protein disulfide-isomerase A3 (sprot)

description: A protein disulfide-isomerase A3 that is encoded in the genome of human.


name: ERAP1_HUMAN Endoplasmic reticulum aminopeptidase 1 (sprot)

description: An endoplasmic reticulum aminopeptidase 1 that is encoded in the genome of human.


CALR_HUMAN Calreticulin (sprot)

A calreticulin that is encoded in the genome of human.


B2MG_HUMAN Beta-2-microglobulin (sprot)

A beta-2-microglobulin that is encoded in the genome of human.


pyridoxal 5'-phosphate(2-)

The dianion resulting from the removal of two protons from the phosphate group of pyridoxal 5'-phosphate.


biotin

An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins.


name: HDAC2_HUMAN Histone deacetylase 2 (sprot)

description: A histone deacetylase 2 that is encoded in the genome of human.


name: HDAC7_HUMAN Histone deacetylase 7 (sprot)

description: A histone deacetylase 7 that is encoded in the genome of human.


name: RFA1_HUMAN Replication protein A 70 kDa DNA-binding subunit (sprot)

description: A replication protein A 70 kDa DNA-binding subunit that is encoded in the genome of human.


An amino-acid betaine gamma-aminobutyric acid zwitterion in which all of the hydrogens attached to the nitrogen are replaced by methyl groups.


Major microspecies at pH 7.3.


CARNITINE

An amino-acid betaine that is butanoate substituted with a hydroxy group at position C-3 and a trimethylammonium group at C-4.


Conjugate base of porphobilinogen arising from deprotonation of the two carboxy groups and protonation of the amino group; major species at pH 7.3.


5-aminolevulinic acid

The simplest delta-amino acid in which the hydrogens at the gamma position are replaced by an oxo group. It is metabolised to protoporphyrin IX, a photoactive compound which accumulates in the skin. Used (in the form of the hydrochloride salt)in combination with blue light illumination for the treatment of minimally to moderately thick actinic keratosis of the face or scalp.


protoporphyrin

A cyclic tetrapyrrole that consists of porphyrin bearing four methyl substituents at positions 3, 8, 13 and 17, two vinyl substituents at positions 7 and 12 and two 2-carboxyethyl substituents at positions 2 and 18. The parent of the class of protoporphyrins.


An acyl-CoA oxoanion that is the pentaanion of succinyl-CoA, arising from deprotonation of the phosphate, diphosphate and carboxylic acid OH groups.


ferroheme b

Heme b in which the iron has oxidation state +2.


Octaanion of preuroporphyrinogen arising from global deprotonation of the eight carboxy groups; major species at pH 7.3.


trans,trans-farnesyl diphosphate

The trans,trans-stereoisomer of farnesyl diphosphate.


The conjugate base of a 1,2-diacyl-sn-glycero-3-phosphocholine compound formed by deprotonation of the phosphate OH group.


name: FNTA_HUMAN Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha (sprot)

description: A protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha that is encoded in the genome of human.


name: RHOA_HUMAN Transforming protein RhoA (sprot)

description: A GTP-binding protein RhoA that is encoded in the genome of human.


name: SC31A_HUMAN Protein transport protein Sec31A (sprot)

description: A protein transport protein Sec31A that is encoded in the genome of human.


name: DYL1_HUMAN Dynein light chain 1, cytoplasmic (sprot)

description: A dynein light chain 1, cytoplasmic that is encoded in the genome of human.


DNLI3_HUMAN DNA ligase 3 (sprot)

A DNA ligase 3 that is encoded in the genome of human.


name: FANCJ_HUMAN Fanconi anemia group J protein (sprot)

description: A Fanconi anemia group J protein that is encoded in the genome of human.


name: ALG1_HUMAN Chitobiosyldiphosphodolichol beta-mannosyltransferase (sprot)

description: A chitobiosyldiphosphodolichol beta-mannosyltransferase that is encoded in the genome of human.


name: ALG2_HUMAN Alpha-1,3/1,6-mannosyltransferase ALG2 (sprot)

description: An alpha-1,3/1,6-mannosyltransferase ALG2 that is encoded in the genome of human.


name: ALG11_HUMAN GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase (sprot)

description: A GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase that is encoded in the genome of human.


name: AG10B_HUMAN Dol-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-Dol alpha-1,2-glucosyltransferase (sprot)

description: A putative Dol-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-Dol alpha-1,2-glucosyltransferase that is encoded in the genome of human.


name: GPT_HUMAN UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase (sprot)

description: A UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase that is encoded in the genome of human.


name: ALG8_HUMAN Dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1,3-glucosyltransferase (sprot)

description: A probable dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1,3-glucosyltransferase that is encoded in the genome of human.


name: ALG9_HUMAN Alpha-1,2-mannosyltransferase ALG9 (sprot)

description: An alpha-1,2-mannosyltransferase ALG9 that is encoded in the genome of human.


name: ALG6_HUMAN Dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase (sprot)

description: A dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase that is encoded in the genome of human.


name: AG10A_HUMAN Dol-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-Dol alpha-1,2-glucosyltransferase (sprot)

description: A Dol-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-Dol alpha-1,2-glucosyltransferase A that is encoded in the genome of human.


name: ALG12_HUMAN Dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase (sprot)

description: A dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl-alpha-1,6-mannosyltransferase that is encoded in the genome of human.


name: ALG3_HUMAN Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase (sprot)

description: A dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichyl mannosyltransferase that is encoded in the genome of human.


name: BAX_HUMAN Apoptosis regulator BAX (sprot)

description: An apoptosis regulator BAX that is encoded in the genome of human.


name: RGS2_HUMAN Regulator of G-protein signaling 2 (sprot)

description: A regulator of G-protein signaling 2 that is encoded in the genome of human.


NADPH

The reduced form of NADP+; used in anabolic reactions, such as lipid and nucleic acid synthesis, which require NADPH as a reducing agent.


An endocannabinoid and an endogenous agonist of the cannabinoid receptors (CB1 and CB2). It is an ester formed from omega-6-arachidonic acid and glycerol.


A 2'-deoxyribonucleoside 5'-triphosphate(4-) arising from deprotonation of the triphosphate OH groups of 2'-deoxycytidine 5'-triphosphate (dCTP); major species at pH 7.3.


ADP-D-ribose

A nucleotide-sugar having ADP as the nucleotide fragment and D-ribofuranos-5-yl as the sugar component.


arachidonate

A long-chain fatty acid anion resulting from the removal of a proton from the carboxy group of arachidonic acid.


Octaanion of 1D-myo-inositol 1,3,4,5-tetrakisphosphate arising from global deprotonation of the phosphate OH groups; major species at pH 7.3.


acetaldehyde

The aldehyde formed from acetic acid by reduction of the carboxy group. It is the most abundant carcinogen in tobacco smoke.


MONOETHANOLAMINE

A member of the class of  ethanolamines that is ethane with an amino substituent at C-1 and a hydroxy substituent at C-2, making it both a primary amine and a primary alcohol.


choline

A choline that is the parent compound of the cholines class, consisting of ethanolamine having three methyl substituents attached to the amino function.


acetylcholine

Actylcholine is an ester of acetic acid and choline, which acts as a neurotransmitter.


chloride

A halide anion formed when chlorine picks up an electron to form an an anion.


nucleoside 5'-triphoshate(4-)

A ribonucleoside triphosphate oxoanion arising from global deprotonation of the  triphosphate groups of any nucleoside triphosphate; major species at pH 7.3.


A 2'-deoxyribonucleoside 5'-triphosphate(4-) that is the tetraanion of 2'-deoxyguanosine 5'-triphosphate (dGTP), arising from deprotonation of the four triphosphate OH groups; major species at pH 7.3.


A 2'-deoxyribonucleoside 5'-triphosphate(4-) obtained by deprotonation of the four triphosphate OH groups of dTTP; major species at pH 7.3.


A 3-sn-glycerophosphoserine compound having acyl substituents at the 1- and 2-hydroxy positions.


1,2-diacyl-sn-glycerol 3-phosphate

An sn-glycerol 3-phosphate compound having unspecified O-acyl groups at the 1- and 2-positions.


The D-threo-form of isocitrate(3-).


hydrogencarbonate

The carbon oxoanion resulting from the removal of a proton from carbonic acid.


S-adenosyl-L-methioninamine

Conjugate acid of S-adenosylmethioninamine arising from protonation of the primary amino group.


L-methionine

The L-enantiomer of methionine.


formate

A monocarboxylic acid anion that is the conjugate base of formic acid. Induces severe metabolic acidosis and ocular injury in human subjects.


2-oxo monocarboxylic acid anion

An oxo monocarboxylic acid anion in which the oxo group is located at the 2-position.


Conjugate base of 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one arising from deprotonation of the 2-hydroxy group.


An ammonium ion obtained by the protonation of all four amino groups of spermine.


Dianion of S-methyl-5-thio-D-ribulose 1-phosphate.


Dianion of S-methyl-5-thio-alpha-D-ribose 1-phosphate.


An ammonium ion that is the trication of spermidine, formed by protonation at all three nitrogens.


The 2-oxo monocarboxylic acid anion derived from 4-methylthio-2-oxobutanoic acid. The major microspecies at pH 7.3, it is formed from L-methionine via the action of methionine transaminase.


Dianion of 5-(methylsulfanyl)-2,3-dioxopentyl phosphate.


METHYLTHIOADENOSINE

Adenosine with the hydroxy group at C-5' substituted with a methylthio (methylsulfanyl) group.


An alkane-alpha,omega-diammonium(2+) that is the dication of putrescine (1,4-butanediamine) arising from protonation of both primary amino groups; major species at pH 7.3.


ferriheme b

Heme b in which the iron has oxidation state +3.


peroxynitrite

The nitrogen oxoanion formed by loss of a proton from peroxynitrous acid.


L-citrulline

The L-enantiomer of citrulline.


nitrite

The nitrogen oxoanion formed by loss of a proton from nitrous acid.


A peptide anion obtained by deprotonation of both carboxy groups and protonation of the glutamyl amino group of glutathione; major species at pH 7.3.


GABA

A gamma-amino acid that is butanoic acid with the amino substituent located at C-4.


The trianion of a 1-phosphatidyl-1D-myo-inositol 5-phosphate.


A phosphatidylinositol 4-phosphate having 1D-myo-configuration.


L-alanine

The L-enantiomer of alanine.


lipid

'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids.


long-chain fatty acid

A fatty acid with a chain length ranging from C13 to C22.


electron

Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.


β-phenylethylamine

A phenylethylamine having the phenyl substituent at the 2-position.


An organic radical cation derived from 5,6,7,8-tetrahydrobiopterin.


L-phenylalanine

The L-enantiomer of phenylalanine.


Tetraanion of 7,8-dihydroneopterin 3'-triphosphate.


The conjugate base of monodehydro-L-ascorbic acid arising from deprotonation of the 4-hydroxy group; major species at pH 7.3.


dyspropterin

A tetrahydropterin  that is 2-amino-5,6,7,8-tetrahydropteridin-4(3H)-one substituted by a 2-oxopropanoyl group at position 6.


A 7,8-dihydrobiopterin in which the 1,2-dihydroxypropyl group has (1S,2R)-configuration.


L-allysine zwitterion

An amino acid zwitterion arising from transfer of a proton from the carboxy to the amino group of L-allysine; major species at pH 7.3.


A  2-acylglycerophosphocholine in which the glycerol moiety has sn stereochemistry and which has an unspecified acyl group attached at the 2-position.


cytidine 5'-monophosphate(2-)

A pyrimidine nucleoside 5'-monophosphate(2-) that results from the removal of two protons from the phosphate group of cytidine 5'-monophosphate; major species at pH 7.3.


acyl-CoA

A thioester that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of any carboxylic acid.


citicoline

A member of the class of  phosphocholines that is the chloine ester of CDP. It is an intermediate obtained in the biosynthetic pathway of structural phospholipids in cell membranes.


phosphatidylethanolamine zwitterion

The zwitterion of a phosphatidylethanolamine compound formed by proton transfer from the phosphate to the primary amino group.


A 1-O-acylglycerophosphoethanolamine having (R)-configuration.


A lysophosphatidylethanolamine obtained by selective hydrolysis of the 1-acyl substituent of any 1,2-diacyl-sn-glycero-3-phosphoethanolamine.


N-arachidonoylphosphatidylethanolamine

An acyl derivative of phosphatidic acid whose phosphorus acid component is esterified with 2-N-arachidonoylaminoethanol.


The ammonium betaine of a 1-O-acyl-sn-glycero-3-phosphocholine arising from deprotonation of the phosphate OH; major species at pH 7.3.


N-acylphosphatidylethanolamine

A phosphatidylethanolamine in which the amine function has formed an amide with a fatty acid RCO2H.


Conjugate base of CDP-ethanolamine arising from deprotonation of the phosphate OH groups and protonation of the amino group; major species at pH 7.3.


acyl group

An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids.


An sn-glycerophosphoserine compound having an acyl substituent at the 1-hydroxy position.


L-serine

The L-enantiomer of serine.


A phosphatidylglycerol consisting of cardiolipin lacking one fatty acyl group from the 2 or 2'-position.


cardiolipin

A phosphatidylglycerol composed of two molecules of phosphatidic acid covalently linked to a molecule of glycerol.


An anionic phospholipid obtained by deprotonation of both free phosphate OH groups of any 2,2'-dilysocardiolipin.


A phosphatidylglycerol(1-) in which the phosphatidyl moiety has R-configuration and the glycerol moiety has S-configuration.


An organophosphate oxoanion arising from deprotonation of both phosphate OH groups of a CDP-diacylglycerol.


A 2-acylglycerophosphoinositol in which sn-glycerol, acylated at O(2), is linked through a phospho group at O(3) to O(1) of D-myo-inositol.


A 1-acylglycerophosphoinositol in which sn-glycerol, acylated at O(1), is linked through a phospho group at O(3) to O(1) of D-myo-inositol.


myo-inositol

An inositol having myo- configuration.


A glyceride in which any one of the R groups (position not specified) is an acyl group while the remaining two R groups can be either H or alkyl groups.


A glycerophosphoglycerol in which sn-glycerol, acylated at O(1), is linked through a phospho group at O(3) to O(1) of glycerol.


A glycerophosphoglycerol in which sn-glycerol, acylated at O(2), is linked through a phospho group at O(3) to O(1) of glycerol.


Trianion of 1-(3-sn-phosphatidyl)-sn-glycerol 3-phosphate arising from deprotonation of all three free phosphate OH groups; major species at pH 7.3.


An ionic phospholipid that is a dianion of a phosphatidic acid arising from deprotonation of both phosphate OH groups.


choline alfoscerate

A member of the class of phosphocholines that is the choline ester of sn-glycero-3-phosphate. It is one of the major osmolyte in the renal medullary cells.


sn-glycerol 3-phosphate(2-)

An organophosphate oxoanion that is the dianion of sn-glycerol 3-phosphate arising from deprotonation of both phosphate OH groups.


name: 2-ammonioethyl (2R)-2,3-dihydroxypropyl phosphate zwitterion

description: Major species at pH 7.3.


phospholipid

A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides.


PHOSPHORYLETHANOLAMINE

The ethanolamine mono-ester of phosphoric acid, and a metabolite of phospholipid metabolism. This phosphomonoester shows strong structural similarity to the inhibitory neurotransmitter GABA, and is decreased in post-mortem Alzheimer's disease brain.


The pentaanion of a 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate.


carboxylic acid

A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.


phosphocholines

Any compound having phosphocholine as part of its structure.


fatty acyl-CoA(4-)

An acyl-CoA(4-) arising from deprotonation of the phosphate and diphosphate OH groups of any fatty acyl-CoA; major species at pH 7.3.


The organophosphate oxoanion obtained by deprotonation of the diphosphate hydroxy groups of the reduced form of flavin adenine dinucleotide (FADH2).


L-homocysteine

A sulfur-containing amino acid consisting of a glycine core with a 2-mercaptoethyl side-chain.


MERCAPTOPURINE

A thiol that is the tautomer of mercaptopurine.


A primary alcohol that is the S-methyl derivative of mercaptoethanol. It is found as a volatile component in Cucumis melo Var. cantalupensis.


A macromolecule consisting of 5-methyltetrahydrofolic acid with an arbitrary number of glutamate residues attached as a polypeptide to the single existent one.


PYRIDINE

An  azaarene comprising a benzene core in which one -CH group is replaced by a nitrogen atom. It is the parent compound of the class pyridines.


A thiopurine that is 9H-purine substituted by a methylsulfanyl group at position 6.


A monohydroxybenzoate that is the conjugate base of 3-hydroxy-4-methoxybenzoic acid, arising from deprotonation of the carboxy group.


PROTOCATECHUIC ACID

A dihydroxybenzoic acid in which the hydroxy groups are located at positions 3 and 4.


glutathione disulfide(2-)

A doubly-charged peptide anion arising from deprotonation of the four carboxy groups and protonation of the two amino groups of glutathione disulfide; major species at pH 7.3.


An ionic macromolecule consisting of (6R)-5,10-methylenetetrahydrofolate(2-) with an arbitrary number of glutamate residues attached as a polypeptide to the single existent one.


adenosine 3',5'-bismonophosphate(4-)

An organophosphate oxoanion arising from deprotonation of the phosphate OH groups of adenosine 3',5'-bismonophosphate; major species at pH 7.3.


3'-phosphonato-5'-adenylyl sulfate(4-)

A quadruply-charged organophosphate oxoanion arising from deprotonation of the phosphate and sufate groups of 3'-phosphonato-5'-adenylyl sulfate; major species at pH 7.3.


paracetamol

A member of the class of phenols that is 4-aminophenol in which one of the hydrogens attached to the amino group has been replaced by an acetyl group.


butyrate

A short-chain fatty acid anion that is the conjugate base of butyric acid, obtained by deprotonation of the carboxy group.


An ammonium ion that is the conjugate acid of dopamine; major species at pH 7.3.


phenol

An organic hydroxy compound that consists of benzene bearing a single hydroxy substituent. The parent of the class of phenols.


A N-substituted amine that is 4-aminobiphenyl substituted by a hydroxy group at the nitrogen atom.


A nucleotide-sugar oxoanion that is a trianion arising from deprotonation of the carboxy and diphosphate OH groups of UDP-alpha-D-glucuronic acid; major species at pH 7.3.


A dicarboxylic acid dianion obtained by deprotonation of the two carboxy groups of bilirubin; major species at pH 7.3.


acetylsalicylate

A benzoate that is the conjugate base of acetylsalicylic acid, arising from deprotonation of the carboxy group.


salicylates

Any salt or ester arising from reaction of the carboxy group of salicylic acid, or any ester resulting from the condensation of the phenolic hydroxy group of salicylic acid with an organic acid.


bis(beta-glucosyluronate)bilirubin

Conjugate base of bis(beta-glucosyluronic acid)bilirubin.


glutathione

A tripeptide compound consisting of glutamic acid attached via its side chain to the N-terminus of cysteinylglycine.


OXIRANE

A  saturated organic heteromonocyclic parent that is a three-membered heterocycle of two carbon atoms and one oxygen atom.


Conjugate base of L-gamma-glutamyl-L-cysteine arising from deprotonation of both carboxy groups and protonation of the primary amino group; major species at pH 7.3.


DINITROCHLOROBENZENE

A C-nitro compound that is chlorobenzene carrying a nitro substituent at each of the 2- and 4-positions.


An S-substituted glutathione(1-) obtained by deprotonation of the the two carboxy groups and protonation of the glutamyl amino group of S-(2,4-dinitrophenyl)glutathione. Major microspecies at pH 7.3.


A member of the class of tetralins obtained by formal epoxidation across the 2,3-double bond of menatetrenone.


menatetrenone

A menaquinone whose side-chain contains 4 isoprene units in an all-trans-configuration.


deoxycholic acid

A bile acid that is 5beta-cholan-24-oic acid substituted by hydroxy groups at positions 3 and 12 respectively.


2-oxobutanoic acid

A 2-oxo monocarboxylic acid that is the 2-oxo derivative of butanoic acid.


cystathionine

A modified amino acid generated by enzymic means from L-homocysteine and L-serine.


3-mercaptopyruvic acid

A 2-oxo monocarboxylic acid that is  pyruvic acid substituted by a sulfanyl group at position 3.


sulfite

A sulfur oxoanion that is the conjugate base of hydrogen sulfite (H2SO3).


ubidecarenone

A ubiquinone having a side chain of 10 isoprenoid units. In the naturally occurring isomer, all isoprenyl double bonds are in the E- configuration.


dolichyl D-mannosyl phosphate(1-)

Conjugate base of dolichyl D-mannosyl phosphate arising from deprotonation of the free OH group of the phosphate.


dolichyl phosphate(2-)

Dianion of dolichyl phosphate arising from deprotonation of both phosphate OH groups.


Conjugate base of GDP-alpha-D-mannose arising from deprotonation of both free OH groups of the diphosphate.


An alpha-amino-acid anion that is the conjugate base of 3-sulfino-L-alanine, arising from deprotonation of the sulfino and carboxy groups and protonation of the amino group; major species at pH 7.3.


taurine

An amino sulfonic acid that is the 2-amino derivative of ethanesulfonic acid. It is a naturally occurring amino acid derived from  methionine and cysteine metabolism. An abundant component of fish- and meat-based foods, it has been used as an oral supplement in the treatment of disorders such as cystic fibrosis and hypertension.


HYPOTAURINE

An aminosulfinic acid comprising ethylamine having the sulfo group at the 2-position.


thiocyanate

A pseudohalide anion obtained by deprotonation of the thiol group of thiocyanic acid.


CYANIDE

A one-carbon compound consisting of a methine group triple bonded to a nitrogen atom


name: (ethanolamineP) mannose (a1-2) (ethanolamineP) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI

description: Is a glycan


An inositol compound having an alpha-mannosyl-(1->2)-alpha-mannosyl-(1->6)-alpha-2-(2-aminoethylphosphoryl)mannosyl-alpha-glucosaminyl moiety at the 6-position, a phosphatidyl substituent at the 1-position and an undefined acyl substituent in an unspecified position.


betaine

The amino acid betaine derived from glycine.


N,N-dimethylglycine zwitterion

An amino acid zwitterion resulting from transfer of a proton from the carboxy to the amino group of N,N-dimethylglycine; major species at pH 7.3.


A 6-O-[alpha-D-mannosyl-(1->4)-alpha-D-glucosaminyl]-1-phosphatidyl-1D-myo-inositol compound having an undefined acyl substituent in an unspecified position on the inositol ring.


An inositol compound having an alpha-mannosyl-(1->6)-alpha-2-(2-aminoethylphosphoryl)mannosyl-alpha-glucosaminyl group at the 6-position, a phosphatidyl group at the 1-position and an undefined acyl substituent at an unspecified position.


A UDP-D-galactose(2-) in which the anomeric centre of the galactose moiety has alpha-configuration.


The cationic sphingoid resulting from the protonation of the amino group of sphingosine.


sphingosine 1-phosphate(1-)

The conjugate base of sphingosine 1-phosphate having an anionic phosphate group and a protonated amino group; major species at pH 7.3.


N-acetyl-D-galactosamine

The D-enantiomer of N-acetylgalactosamine.


A diosylceramide having beta-D-galactosyl-(1->4)-beta-D-glucose as the disaccharide component.


N-acylsphingosine 1-phosphate

A ceramide phosphate compound having the phosphate group in the 1-position and an unspecified acyl group atached to the nitrogen atom.


Dianion of UDP-N-acetyl-D-galactosamine arising from deprotonation of the diphosphate OH groups; major species at pH 7.3.


A glycotriaosylceramide having alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucose as the trisaccharide component.


D-glucosyl-N-acylsphingosine

Sphingosine substituted at the 1-hydroxy group by a D-glucosyl group and at the 2-amino group by an acyl group.


N-acyl-beta-D-galactosylsphingosine

An N-acyl-D-galactosylsphingosine in which the anomeric configuration of the galactosyl residue is beta; sphingosine substituted at the O-1 position by a beta-D-galactosyl group and at the N-2 position by an acyl group.


A sialodiosylceramide consisting of the trisaccharide alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->4)-beta-D-Glc attached to the primary hydroxy function of ceramide.


N-acetylneuraminic acid

An N-acylneuraminic acid where the N-acyl group is specified as acetyl.


An N-acetylneuraminate that is the conjugate base of beta-D-GalNAc-(1->4)-[alpha-Neu5Ac-(2->3)]-beta-D-Gal-(1->4)-beta-D-Glc-(1<->1')-Cer, obtained by deprotonation of the carboxy group; major species at pH 7.3.


D-glucitol 6-phosphate

The 6-O-phospho derivative of D-glucitol.


D-glucopyranose 1-phosphate(2-)

An organophosphate oxoanion that is the dianion of D-glucopyranose 1-phosphate arising from deprotonation of both phosphate OH groups.


L-cysteinylglycine zwitterion

The zwitterion of L-cysteinylglycine resulting from the transfer of a proton from the hydroxy group of glycine to the amino group of cysteine. Major microspecies at pH 7.3.


Conjugate base of 5-oxo-L-proline.


uridine 5'-monophosphate(2-)

A pyrimidine nucleoside 5'-monophosphate(2-) that results from the removal of two protons from the phosphate group of UMP.


guanosine 5'-monophosphate(2-)

A nucleoside 5'-monophosphate(2-) that results from the removal of two protons from the phosphate group of GMP.


SALICYLURIC ACID

An N-acylglycine in which the acyl group is specified as 2-hydroxybenzoyl.


L-glutamine

An optically active form of glutamine having L-configuration.


A hydroxyaldehyde consisting of phenylacetaldehyde having three hydroxy substituents located at the alpha-, 3- and 4-positions. It is a metabolite of noradrenaline.


levodopa

An optically active form of dopa having L-configuration. Used to treat the stiffness, tremors, spasms, and poor muscle control of Parkinson's disease


The anion obtained from global deprotonation of the phosphate OH groups of myo-inositol 1,3,4,5,6-pentakisphosphate; major species at pH 7.3.


myo-inositol hexakisphosphate(12-)

The organophosphate oxoanion formed by loss of 2 protons from each of the phosphate groups of 1D-myo-inositol.


Fully deprotonated form of 5-diphospho-1D-myo-inositol pentakisphosphate.


Octaanion of 1D-myo-inositol 3,4,5,6-tetrakisphosphate arising from global deprotonation of the acidic phosphate OH groups.


1D-myo-inositol 1,3,4-trisphosphate(6-)

The hexaanion of 1D-myo-inositol 1,3,4-trisphosphate.


An organophosphate oxoanion obtained by deprotonation of all but one of the phosphate and diphosphate OH groups of 1,5-bis(diphospho)-1D-myo-inositol 2,3,4,6-tetrakisphosphate. It is the major microspecies at pH 7.3 (according to Marvin v 6.2.0.).


Octaanion of myo-inositol 1,3,4,6-tetrakisphosphate arising from global deprotonation of the phosphate OH groups; major species at pH 7.3.


A myo-inositol tetrakisphosphate that consists of myo-inositol having the four phospho groups located at positions 2, 3, 4 and 6 as well as a diphospho group at position 5.


An inositol phosphate oxoanion obtained by global deprotonation of the phosphate and diphosphate OH groups of 1-diphospho-1D-myo-inositol 2,3,4,5,6-pentakisphosphate.


A 1D-myo-inositol bis(diphosphate) trisphosphate having the three phospho groups located at positions 3, 4 and 6 and the two diphospho groups at positions 1 and 5.


A myo-inositol pentakisphosphate that consists of myo-inositol having the five phospho groups located at positions 1, 2, 3, 4 and 6 as well as a triphospho group at position 5.


1D-myo-inositol 3,4,6-trisphosphate

A myo-inositol trisphosphate having the three phosphate groups at the 3-, 4-, and 6-positions.


A myo-inositol tetrakisphosphate that consists of myo-inositol having the four phospho groups located at positions 3, 4, 5 and 6 as well as a diphospho group at position 1.


aldehydo-D-galactose

An aldohexose that is the C-4 epimer of glucose.


MALTOTRIOSE

A maltotriose trisaccharide in which the glucose residue at the reducing end is in the pyranose ring form and has alpha configuration at the anomeric carbon atom..


maltose

A glycosylglucose consisting of two D-glucopyranose units connected by an alpha-(1->4)-linkage.


D-fructose

Fructose is a levorotatory monosaccharide and an isomer of glucose.  Although fructose is a hexose (6 carbon sugar), it generally exists as a 5-member hemiketal ring (a furanose).


lactose

A glycosylglucose disaccharide, found most notably in milk, that consists of D-galactose and D-glucose fragments bonded through a beta-1->4 glycosidic linkage. The glucose fragment can be in either the alpha- or beta-pyranose form, whereas the galactose fragment can only have the beta-pyranose form.


uroporphyrinogen I(8-)

The cyclic tetrapyrrole anion that is the octacarboxylate anion of uroporphyrinogen I.


coproporphyrinogen I(4-)

The cyclic tetrapyrrole anion formed by loss of a proton from each of the four carboxy groups of coproporphyrinogen I.


chemical entity

A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.


Dicarboxylate anion of biliverdin; major species at pH 7.3.


CARBON MONOXIDE

A one-carbon compound in which the carbon is joined only to a single oxygen. It is a colourless, odourless, tasteless, toxic gas.


GDP-fucose

A GDP-fucose in which the fucosyl residue has L-configuration.


Dianion of CMP-N-acetyl-beta-neuraminate arising from deprotonation of carboxylic acid and phosphate functions; major species at pH 7.3.


A C21-steroid that is pregnane which contains a double bond between positions 5 and 6 and is substituted by oxo groups at positions 3 and 20.


androstenedione

A 3-oxo Delta(4)-steroid that is androst-4-ene substituted by oxo groups at positions 3 and 17. It is a steroid hormone synthesized in the adrenal glands and gonads.


testosterone

An androstanoid having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5..


deoxycorticosterone

A mineralocorticoid that is progesterone substituted at position 21 by a hydroxy group.


A 18-hydroxy steroid that is corticosterone substituted by a hydroxy group at position 18.


aldosterone

A pregnane-based steroidal hormone produced by the outer-section (zona glomerulosa) of the adrenal cortex in the adrenal gland, and acts on the distal tubules and collecting ducts of the kidney to cause the conservation of sodium, secretion of potassium, increased water retention, and increased blood pressure. The overall effect of aldosterone is to increase reabsorption of ions and water in the kidney.


corticosterone

A 21-hydroxy steroid that consists of pregn-4-ene substituted by hydroxy groups at positions 11 and 21 and oxo groups at positions 3 and 20. Corticosterone is a 21-carbon steroid hormone of the corticosteroid type produced in the cortex of the adrenal glands.


cortisol

A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses.


A C21-steroid that is pregnane which contains a double bond between positions 5 and 6 and is substituted by oxo groups at positions 3 and 20 as well as a hydroxy group at position 17.


isopentenyl diphosphate

A prenol phosphate comprising 3-methylbut-3-en-1-ol having an O-diphosphate substituent.


DIMETHYLALLYL DIPHOSPHATE

A prenol phosphate that is a phosphoantigen comprising the O-pyrophosphate of prenol.


geranyl diphosphate

The diphosphate of the polyprenol compound geraniol.


A steroid acid, the 4-carboxy-4-methyl derivative of zymosterol.


A steroid acid, the 4-carboxy derivative of zymosterol.


A 3beta-hydroxy steroid, the 4-methyl derivative of zymosterol.


presqualene diphosphate

A triterpenyl phosphate that is presqualene in which the hydroxy hydrogen has been replaced by a diphosphate group.


A 3beta-sterol formed from lanosterol by reduction across the C-24-C-25 double bond.


The 5-diphospho derivative of (R)-mevalonic acid.


A cholestanoyl-CoA formed by thioester linkage between 3alpha,7alpha,24-trihydroxy-5beta-cholestanoic acid and coenzyme A.


An acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of (24R,25R)-3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestan-26-oic acid.


propionyl-CoA

An acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of propionic acid.


A steroidal acyl-CoA(4-) resulting from the removal of all four protons from the phosphate groups of chenodeoxycholoyl-CoA. Major species at pH 7.3.


A steroidal acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-en-26-oic acid.


A cholestanoyl-CoA formed by thioester linkage between  3alpha,7alpha,12alpha-trihydroxy-24-oxo-5beta-cholestan-26-oic acid and coenzyme A.


A cholestanoyl-CoA formed by thioester linkage between 3alpha,7alpha-dihydroxy-24-oxo-5beta-cholestan-26-oic acid and coenzyme A.


An organophosphate oxoanion that is the trianion of (R)-5-phosphopantothenic acid arising from deprotonation of the carboxy and phosphate OH groups; major species at pH 7.3


PANTOTHENIC ACID, RACEMIC

A member of the class of pantothenic acids that is an amide formed from pantoic acid and beta-alanine.


Trianion of N-[(R)-4-phosphopantothenoyl]-L-cysteine arising from deprotonation of carboxylic acid and phosphate functions.


An adenosine 5'-phosphate that is coenzyme A in which the phosphate group at position 3' has been replaced by a hydrogen atom. It is an intermediate metabolite in pantothenate and CoA biosynthesis.


thiamine(1+) diphosphate(3-)

Dianion of thiamine(1+) diphosphate arising from deprotonation of the three OH groups of the diphosphate.


thiamine(1+) triphosphate

A thiamine phosphate that is thiamine(1+) in which the hydroxy group is replaced by a triphosphate group. It is found in low amounts in most vertebrate tissues and can phosphorylate certain proteins.


L-dehydroascorbate

An organic anion and the conjugate base of L-dehydroascorbic acid, arising from deprotonation of the acidic C2-position.


The trianion arising from deprotonation of the diphosphate hydroxy groups and the imide nitrogen of flavin mononucleotide (FMN). Major species at pH 7.3.


An optically active form of lysinium having L-configuration.


biocytin

A  monocarboxylic acid amide that results from the formal condensation of the carboxylic acid group of biotin with the N(6)-amino group of L-lysine.


nicotinic acid D-ribonucleotide

A D-ribonucleotide having nicotinic acid as the nucleobase.


NICOTINAMIDE RIBOSIDE

A pyridine nucleoside consisting of nicotinamide with a beta-D-ribofuranosyl moiety at the 1-position.


A dicarboxylic acid monoanion that is the conjugate base of 2-amino-3-(3-oxoprop-1-enyl)but-2-enedioic acid and the major microspecies at pH 7.3 (according to Marvin v 6.2.0.).


3-hydroxyanthranilic acid

An  aminobenzoic acid that is benzoic acid substituted at C-2 by an amine group and at C-3 by a hydroxy group. It is an intermediate in the metabolism of the amino acid tryptophan.


Dianion of 10-formyltetrahydrofolic acid arising from deprotonation of both carboxylic acid functions.


A tetrahydrofolyl glutamate consisting of a tetrahydrofolyl group linked via an amide bond to a poly(gamma-glutamyl chain)


Dianion of dihydrofolic acid arising from deprotonation of both carboxylic acid functions.


(6S)-5,6,7,8-tetrahydrofolic acid

A derivative of folic acid in which the pteridine ring is fully reduced; it is the parent compound of a variety of coenzymes that serve as carriers of one-carbon groups in metabolic reactions.


Dianion of (6S)-5,6,7,8-tetrahydrofolic acid arising from deprotonation of both carboxylic acid functions.


A macromolecule consisting of 10-formyltetrahydrofolic acid with an arbitrary number of glutamate residues attached as a polypeptide to the single existent one.


sarcosine

A N-alkylglycine that is the N-methyl derivative of glycine. It is an intermediate in the metabolic pathway of glycine.


A dicarboxylic acid anion arising from deprotonation of both carboxylic acid functions of (6R)-5,10-methenyltetrahydrofolic acid.


An ionic macromolecule consisting of (6R)-5,10-methenyltetrahydrofolate(2-) with an arbitrary number of glutamate residues attached as a polypeptide to the single existent one.


A pyridinium ion comprising nicotinamide having a methyl group at the 1-position. It is a metabolite of nicotinamide which was initially considered to be biologically inactive but has emerged as an anti-thrombotic and anti-inflammatory agent.


(S)-NADPHX

A tetrahydronicotinamide adenine dinucleotide obtained by formal stereo- and regioselective hydration across the 2,3-double bond in the nicotinyl ring of NADPH, with the hydroxy group located at position 2, having (S)-configuration.


A linear trisaccharide glycosyl group consisting of two galactosyl residues linked to a xylosyl residue at the reducing end.


A linear hexasaccharide glycosyl group consisisting of one iduronic acid residue sulfated on O-2, one glucosamine residue sulfated on nitrogen and at O-3, one glucuronic acid residue, and two galactose residues linked to a xylosyl residue at the reducing end and which is commonly bonded to an amino acid residue.


An aspartate(1-) that is the  conjugate base of L-aspartic acid.


A linear heptasaccharide glycosyl group consisisting of one iduronic acid residue sulfated on O-2, two glucosamine residues, of which one is N-acetylated and the other is sulfated on nitrogen and at O-3, one glucuronic acid residue, and two galactose residues linked to a xylosyl residue at the reducing end and which is commonly bonded to an amino acid residue.


A linear tetrasaccharide glycosyl group consisting of one galacturonic acid resiue and two galactosyl residues linked to a xylosyl residue at the reducing end.


aldehydo-N-acetyl-D-glucosamine

The open-chain form of N-acetyl-D-glucosamine.


A linear pentasaccharide glycosyl group consisisting of one N-acetylglucosamine residue, one glucuronic acid residue and two galactose residues linked to a xylosyl residue at the reducing end and which is commonly bonded to an amino acid residue.


A linear hexasaccharide glycosyl group consisisting of one iduronic acid residue, one glucosamine residue sulfated on nitrogen and at O-3, one glucuronic acid residue, and two galactose residues linked to a xylosyl residue at the reducing end and which is commonly bonded to an amino acid residue.


A linear pentasaccharide glycosyl group consisisting of one glucosamine residue sulfated on nitrogen and at O-3, one glucuronic acid residue, and two galactose residues linked to a xylosyl residue at the reducing end and which is commonly bonded to an amino acid residue.


A linear heptasaccharide glycosyl group consisisting of one iduronic acid residue sulfated on O-2, two glucosamine residues, both sulfated on nitrogen and with one also sulfated at O-3 and the other sulfated at O-6, one glucuronic acid residue, and two galactose residues linked to a xylosyl residue at the reducing end and which is commonly bonded to an amino acid residue.


A linear heptasaccharide glycosyl group consisisting of one iduronic acid residue sulfated on O-2, two glucosamine residues, one of which is sulfated on nitrogen and at O-3, one glucuronic acid residue, and two galactose residues linked to a xylosyl residue at the reducing end and which is commonly bonded to an amino acid residue.


A linear pentasaccharide glycosyl group consisisting of one glucosamine residue, one glucuronic acid residue, and two galactose residues linked to a xylosyl residue at the reducing end and which is commonly bonded to an amino acid residue.


aldehydo-L-iduronate

An iduronate that is the conjugate base of aldehydo-L-iduronic acid, obtained by deprotonation of the carboxy group; major species at pH 7.3.


A linear octasaccharide glycosyl group consisisting of two iduronic acid residues, one of which is sulfated on O-2, two glucosamine residues, both sulfated on nitrogen and with one also sulfated at O-3 and the other sulfated at O-6, one glucuronic acid residue, and two galactose residues linked to a xylosyl residue at the reducing end and which is commonly bonded to an amino acid residue.


D-glucuronic acid

The D-enantiomer of glucuronic acid.


An amino hexasaccharide comprising an iduronic acid residue, an acetylated galactosamine residue, sulfated on O-4, a glucuronic acid residue, and two galactose residues, linked to a xylose residue at the reducing end. It is an intermediate in the dermatan sulfate degradation pathway.


A linear heptasaccharide glycosyl group consisting of two N-acetylgalactosamine residues, two glucuronic acid residues and two galactosyl residues linked to a xylosyl residue at the reducing end.


A linear heptasaccharide glycosyl group consisting of two N-acetylgalactosamine residues (one of which is sulfated at the 4-position), one iduronic acid residue, one glucuronic acid residue and two galactosyl residues linked to a xylosyl residue at the reducing end.


A linear heptasaccharide glycosyl group consisting of two N-acetylgalactosamine residues (one of which is sulfated at the 4-position), one iduronic acid residue sulfated at the 2-position, one glucuronic acid residue and two galactosyl residues linked to a xylosyl residue at the reducing end.


An amino pentasaccharide comprising an N-acetylated galactosamine residue, sulfated on O-4, a glucuronic acid residue and two galactose residues, linked to a xylose residue at the reducing end. It is an intermediate in the chondroitin sulfate degradation pathway.


myristoyl-CoA

A long-chain fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of myristic acid.


An unsaturated fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of (9Z,12Z,15Z,18Z,21Z)-tetracosapentaenoic acid. It is a member of the n-3 PUFA and is the product of alpha-linolenic acid metabolism.


An unsaturated fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of (6Z,9Z,12Z,15Z,18Z,21Z)-tetracosahexaenoic acid. It is a member of n-3 PUFA and a product of alpha-linolenoic acid metabolism.


alpha-linolenoyl-CoA

An octadecatrienoyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of alpha-linolenic acid.


An unsaturated fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of (7Z,10Z,13Z,16Z,19Z)-docosapentaenoic acid. It is a member of n-3 PUFA and a product of alpha-linolenic acid metabolism


An unsaturated fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of (6Z,9Z,12Z,15Z)-octadecatetraenoic acid. It is a member of the n-3 PUFA and is the product of alpha-linolenic acid metabolism.


An unsaturated fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of (8Z,11Z,14Z,17Z)-icosatetraenoic acid. It is a member of the n-3 PUFA and is the product of alpha-linolenic acid metabolism.


An unsaturated fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of (6Z,9Z,12Z,15Z,18Z,21Z)-3-hydroxytetracosahexaenoic acid. It is a member of n-3 PUFA and a product of alpha-linolenoic acid metabolism.


An unsaturated fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of (5Z,8Z,11Z,14Z,17Z)-icosapentaenoic acid. It is a member of n-3 PUFA and by-product of alpha-linolenic acid metabolism.


An unsaturated fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of (2E,6Z,9Z,12Z,15Z,18Z,21Z)-tetracosaheptaenoic acid. It is a member of n-3 PUFA and a product of alpha-linolenoic acid metabolism.


An unsaturated fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of (6Z,9Z,12Z,15Z,18Z,21Z)-3-oxotetracosahexaenoic acid. It is a member of n-3 PUFA and a product of alpha-linolenoic acid metabolism.


A polyunsaturated fatty acid anion that is the conjugate base of (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoic acid, obtained by deprotonation of the carboxy group; major species at pH 7.3.


An unsaturated fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoic acid. It is a member of n-3 PUFA and a product of alpha-linolenoic acid metabolism.


α-linolenic acid

A linolenic acid with cis-double bonds at positions 9, 12 and 15. Shown to have an antithrombotic effect.


An unsaturated fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of (7Z,10Z,13Z,16Z)-docosatetraenoic acid. It is a member of the n-6 PUFA and is the product of linoleic acid metabolism.


An unsaturated fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of all-cis-icosa-8,11,14-trienoic acid.


An unsaturated fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of (6Z,9Z,12Z,15Z,18Z)-tetracosapentaenoic acid. It is a member of the n-6 PUFA and is the product of linoleic acid metabolism.


The all-cis-isomer of a C22 polyunsaturated fatty acid having five double bonds in the 4-, 7-, 10-, 13- and 16-positions. It is a member of n-6 PUFA and a product of linoleic acid metabolism.


An unsaturated fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of (9Z,12Z,15Z,18Z)-tetracosatetraenoic acid. It is a member of the n-6 PUFA and is the product of linoleic acid metabolism.


gamma-linolenoyl-CoA

An octadecatrienoyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of gamma-linolenic acid.


An acyl-CoA(4-) arising from deprotonation of the phosphate and diphosphate functions of arachidonoyl-CoA.


linoleoyl-CoA

An octadecadienoyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of linoleic acid.


linoleic acid

An octadecadienoic acid in which the two double bonds are at positions 9 and 12 and have Z (cis) stereochemistry.


L-tyrosine zwitterion

An amino acid zwitterion arising from transfer of a proton from the carboxy to the amino group of L-tyrosine; major species at pH 7.3.


A tetrahydropterin that is 5,6,7,8-tetrahydrobiopterin carrying an additional hydroxy substituent at the 4a-position.


melatonin

A member of the class of  acetamides that is acetamide in which one of the hydrogens attached to the nitrogen atom is replaced by a 2-(5-methoxy-1H-indol-3-yl)ethyl group. It is a hormone secreted by the pineal gland in humans.


N-acetylserotonin

An N-acylserotonin resulting from the formal condensation of the primary amino group of serotonin with the carboxy group of acetic acid.


IOTYROSINE

The monoiodotyrosine that is L-tyrosine carrying an iodo-substituent at position C-3 of the benzyl group.


An alpha-amino-acid anion that is the conjugate base of 3,5-diiodo-L-tyrosine.


IODIDE

A diatomic molecule containing covalently bonded hydrogen and iodine atoms.


The L-enantiomer of thyroxine.


iodine

Molecule comprising two covalently bonded iodine atoms with overall zero charge..


all-trans-4-hydroxyretinoic acid

A retinoid that consists of all-trans-retinoic acid bearing a hydroxy substituent at position 4 on the cyclohexenyl ring.


tretinoin

A retinoic acid in which all four exocyclic double bonds have E- (trans-) geometry.


lauric acid

A straight-chain, twelve-carbon medium-chain saturated fatty acid with strong bactericidal properties; the main fatty acid in coconut oil and palm kernel oil.


histaminium

An ammonium ion that is the conjugate acid of histamine protonated on the side-chain nitrogen.


METHYL ALCOHOL

The primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and an alcohol group.


A HETE that consists of arachidonic acid bearing a hydroxy substituent at position 19.


A hydroxy monocarboxylic acid consisting of icosa-5,9,14-trienoic acid having three hydroxy groups placed at the 8-, 11- and 12-positions.


The 20-hydroxy derivative of leukotriene B4.


A leukotriene composed of (6Z,8E,10E,14Z)-icosatetraenoic acid having (5S)- and (12R)-hydroxy substituents. It is a lipid mediator of inflammation that is generated from arachidonic acid via the 5-lipoxygenase pathway.


A leukotriene that is the (5S,6S)-epoxy derivative of (7E,9E,11Z,14Z)-icosa-7,9,11,14-tetraenoic acid.


thromboxane A2

A thromboxane which is produced by activated platelets and has prothrombotic properties: it stimulates activation of new platelets as well as increases platelet aggregation.


An icosatetraenoic acid in which the double bonds are located at the 6-7, 8-9, 11-12, and 14-15 positions and have E, Z, Z, and Z geometry, respectively, and in which the pro-S hydrogen is substituted by a hydroperoxy group.


An oxoicosatetraenoic acid having a 5-oxo group; and (6E)-, (8Z), (11Z)- and (14Z)-double bonds.


A HETE having a (5S)-hydroxy group and (6E)-, (8Z)-, (11Z)- and (14Z)-double bonds.


A HPETE that is (5Z,8Z,10E,12R,14Z)-icosa-5,8,10,14-tetraenoic acid with the hydroperoxy group located at position 12 (the R-enantiomer).


The (S)-enantiomer of 12-HPETE.


A HETE having a (12R)-hydroxy group and (5Z)-, (8Z)-, (10E)- and (14Z)-double bonds.


A HETE having a (12S)-hydroxy group and (5Z)-, (8Z)-, (10E)- and (14Z)-double bonds.


hepoxilin A3

A hepoxilin having (5Z,9E,14Z) double bond stereochemistry, an 8-hydroxy substituent and an 11S,12S-epoxy group.


The (S)-enantiomer of 15-HPETE.


An oxoicosatetraenoic acid having (5Z,8Z,11Z,13E) double bond stereochemistry, and an oxo group in position 15.


An optically active form of 15-HETE having 15(S)-configuration..


An optically active form of 15-HETE having 15(R)-configuration.


13,14-dihydro-15-oxolipoxin A4

A C20 hydroxy fatty acid obtained by formal hydrogenation across the 13,-14-double bond of 15-oxolipoxin A4.


A C20 hydroxy fatty acid having (5S)-, (6R)- and (15S)-hydroxy groups as well as (7E)- (9E)-, (11Z)- and (13E)-double bonds.


15-oxolipoxin A4

A C20 hydroxy fatty acid having (5S)- and (6R)- -hydroxy groups as well as a 15-oxo group and (7E)- (9E)-, (11Z)- and (13E)-double bonds.


An amino disaccharide consisting of N-acetyl-D-glucosamine having a beta-D-glucuronosyl residue attached at the 3-position.


A 3-demethylubiquinol in which the polyprenyl chain contains 10 prenyl units.


A polyprenylhydroquinone in which the polyprenyl substituent is decaprenyl at C-2; additional methyl and methoxy groups are also present at positions C-3 and C-6 respectively.


A monohydroxybenzoic acid that is 4-hydroxybenzoic acid in which the hydrogens at positions 3 and 5 are substituted by a methoxy and a decaprenyl group.


A polyprenylhydroquinone in which the polyprenyl substituent is decaprenyl at C-2; a methoxy group is also present at C-6.


A ubiquinol in which the polyprenyl substituent is decaprenyl.


3-decaprenyl-4,5-dihydroxybenzoic acid

A dihydroxybenzoic acid that is 3,4-dihydroxybenzoic acid in which the hydrogen at position 5 is substituted by a decaprenyl group.


PARABEN

A monohydroxybenzoic acid that is benzoic acid carrying a hydroxy substituent at C-4 of the benzene ring.


A monohydroxybenzoic acid that is 4-hydroxybenzoic acid in which the hydrogen at position 3 is substituted by a decaprenyl group.


all-trans-decaprenyl diphosphate

A decaprenyl diphosphate having (E)-stereochemistry exclusively in the double bonds.


LEUKOTRIENE D4

A leukotriene that is (7E,9E,11Z,14Z)-icosa-7,9,11,14-tetraenoic acid substituted by a hydroxy group at position 5 (5S) and a L-cysteinylglycinyl group at position 6 (6R).


12-dehydro-leukotriene B4

A long-chain fatty acid consisting of leukotriene B4 having a 12-keto group in place of the 12-hydroxy group.


eoxin C4

A leukotriene that is the 14R-(S-glutathionyl),15S-hydroxy derivative of (5Z,8Z,10E,12E)-icosa-7,9,11,14-tetraenoic acid.


eoxin E4

A leukotriene that is the 14R-(S-cysteinyl),15S-hydroxy derivative of (5Z,8Z,10E,12E)-icosa-7,9,11,14-tetraenoic acid.


eoxin A4

An oxylipin that is the (14S,15S)-epoxy derivative of (5Z,8Z,10E,12E)-icosa-5,8,10,12-tetraenoic acid.


A leukotriene that is (5S,7E,9E,11Z,14Z)-5-hydroxyicosa-7,9,11,14-tetraenoic acid in which a glutathionyl group is attached at position 6 via a sulfide linkage.


20-hydroxy-20-oxoleukotriene B4

A member of the class of leukotrienes that is leukotriene B4 in which the terminal methyl group has undergone formal oxidation to the corresponding carboxylic acid.


LEUKOTRIEN E4

A leukotriene that is (7E,9E,11Z,14Z)-icosa-7,9,11,14-tetraenoic acid substituted by a hydroxy group at position 5 (5S) and an L-cystein-S-yl group at position 6 (6R).


eoxin D4

A leukotriene that is the 14R-(S-cysteinylglycyl),15S-hydroxy derivative of (5Z,8Z,10E,12E)-icosa-7,9,11,14-tetraenoic acid.


18-hydroxy-18-oxo-dinorleukotriene B4

An octadecatetraenedioic acid obtained by oxidative degradation of leukotriene B4, a process that results in the removal of C19 and C20 with concomitant dioxygenation of C18.


20-oxoleukotriene B4

A leukotriene that is leukotriene B4 bearing an additional oxo substituent at position 20.


A HETE that consists of arachidonic acid bearing a hydroxy substituent at position 20.


A nucleoside 5'-monophosphate(2-) that results from the removal of two protons from the phosphate group of IMP; major species at pH 7.3.


A member of the class of prostaglandins J that is prosta-5,9,12-trien-1-oic acid carrying oxo and hydsroxy substituents at positions 11 and 15 respectively (the 5Z,12E,15S-stereoisomer).


prostaglandin C2

A member of the class of prostaglandins C that is prosta-5,11,13-trien-1-oic acid carrying oxo and hydroxy substituents at positions 9 and 15 respectively (the 5Z,13E,15S-stereoisomer).


11-epi-prostaglandin F2alpha

The prostaglandin F that is the 11-epimer of prostaglandin F2alpha.


15-deoxy-Delta(12,14)-prostaglandin D2

A prostaglandin D derivative that is prostaglandin D2 lacking the 15-hydroxy group and having C=C double bonds at positions 12(13) and 14(15).


THROMBOXANE B2

A member of the class of thromboxanes B that is (5Z,13E)-thromboxa-5,13-dien-1-oic acid substituted by hydroxy groups at positions 9, 11 and 15.


15-deoxy-Delta(12,14)-prostaglandin A2

A prostaglandin A derivative that is prostaglandin A2 lacking the 15-hydroxy group and having C=C double bonds at positions 12(13) and 14(15).


6-oxoprostaglandin F1alpha

A prostaglandin Falpha that is prostaglandin F1alpha bearing a keto substituent at the 6-position.


PROSTAGLANDIN D2

A member of the class of  prostaglandins D that is prosta-5,13-dien-1-oic acid substituted by hydroxy groups at positions 9 and 15 and an oxo group at position 11 (the 5Z,9alpha,13E,15S- stereoisomer).


MALONALDEHYDE

A dialdehyde that is propane substituted by two oxo groups at the terminal carbon atoms respectively. A biomarker of oxidative damage to lipids caused by smoking, it exists in vivo mainly in the enol form.


12-hydroxyheptadecatrienoic acid

A trienoic fatty acid that consists of (5Z,8E,10E)-heptadeca-5,8,10-trienoic acid bearing an additional 12S-hydroxy substituent.


11-dehydro-thromboxane B2

A thromboxane obtained by formal oxidation of the hemiacetal hydroxy function of thromboxane B2.


A member of the class of prostaglandins J that consists of prosta-5,9,13-trien-1-oic acid substituted by an oxo group at position 11 and a hydroxy group at position 15 (the 5Z,13E,15S stereoisomer).


A prostaglandins Falpha that is prosta-5,13-dien-1-oic acid substituted by hydroxy groups at positions 9, 11 and 15. It is a naturally occurring prostaglandin used to induce labor.


15-deoxy-Δ-12,14-prostaglandin J2

A prostaglandin J derivative comprising prostaglandin J2 lacking the 15-hydroxy group and having C=C double bonds at the 12- and 14-positions.


A retinal having 2E,4Z,6E,8E-double bond geometry.


all-trans-retinal

A retinal in which all four exocyclic double bonds have E- (trans-) geometry.


photon

Particle of zero charge, zero rest mass, spin quantum number 1, energy hnu and momentum hnu/c (h is the Planck constant, nu the frequency of radiation and c the speed of light), carrier of electromagnetic force.


A glutathione conjugate obtained by formation of a thioselenide link between the thiol group of glutathione and the selenol group of 1-seleno-N-acetyl-D-galactosamine.


methylselenol

An organoselenium compound that is a selenium analogue of methanol, comprising a methyl group covalently bound to a selenol group.


A glycal derivative that is 1,5-anhydro-2-deoxy-D-arabino-hex-1-enitol substituted by an acetylamino group at position 2.


A monosaccharide derivative that is  N-acetyl-beta-D-galactosamine in which the anomeric hydroxy group is replaced by a methylseleno group.


METHYLSELENINIC ACID

An organoselenium compound that is seleninic acid in which the hydrogen attached to selenium is replaced by a methyl group.


A carboxylic acid anion resulting from the deprotonation of all four carboxy groups and the protonation of both of the primary amino groups of selenodiglutathione. The major species at pH 7.3.


N-acetyl-beta-D-galactosaminyl group

The glycosyl group obtained by removing the hydroxy group from the hemiacetal function of N-acetyl-beta-D-galactosamine.


glutathioselenol

A glutathione derivative that is glutathione in which the hydrogen attached to the sulfur is replaced by a selenol group.


N-acetyl-beta-D-galactosamine

An N-acetyl-D-galactosamine having beta-configuration at the anomeric centre.


A nucleoside 5'-diphosphate(3-) arising from deprotonation of all three OH groups of the diphosphate function of of inosine 5'-diphosphate (IDP); major species at pH 7.3.


A nucleoside 5'-monophosphate(2-) that results from the removal of two protons from the phosphate group of N(6)-methyl-AMP.


Major microspecies at pH 7.3


L-selenohomocysteine

A selenoamino acid that is the selenium analogue of L-homocysteine.


L-adenosylselenomethionine

A selenomethionine consisting of L-selenomethionine having an adenosyl group attached to the selenium.


L-adenosylselenohomocysteine

A selenoamino acid that is L-selenomethionine in which the methyl group attached to the selenium is replaced by a 5'-adenosyl group.


methylselenenic acid

An organoselenium compound comprising a methyl and hydroxy group covalently bound to a selenium atom.