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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-14 16:20:51 UTC
Update Date2022-11-30 20:06:51 UTC
HMDB IDHMDB0289763
Secondary Accession NumbersNone
Metabolite Identification
Common NamePC(P-18:1(9Z)/PGD2)
DescriptionPC(P-18:1(9Z)/PGD2) is an oxidized phosphatidylcholine (PC or GPCho). Oxidized phosphatidylcholines are glycerophospholipids in which a phosphorylcholine moiety occupies a glycerol substitution site and at least one of the fatty acyl chains has undergone oxidation. As all oxidized lipids, oxidized phosphatidylcholines belong to a group of biomolecules that have a role as signaling molecules. The biosynthesis of oxidized lipids is mediated by several enzymatic families, including cyclooxygenases (COX), lipoxygenases (LOX) and cytochrome P450s (CYP). Non-enzymatically oxidized lipids are produced by uncontrolled oxidation through free radicals and are considered harmful to human health (PMID: 33329396 ). As is the case with diacylglycerols, glycerophosphocholines can have many different combinations of fatty acids of varying lengths, saturation and degrees of oxidation attached at the C-1 and C-2 positions. PC(P-18:1(9Z)/PGD2), in particular, consists of one chain of one 1Z,9Z-octadecadienyl at the C-1 position and one chain of Prostaglandin D2 at the C-2 position. Phospholipids are ubiquitous in nature and are key components of the lipid bilayer of cells, as well as being involved in metabolism and signaling. Similarly to what occurs with phospholipids, the fatty acid distribution at the C-1 and C-2 positions of glycerol within oxidized phospholipids is continually in flux, owing to phospholipid degradation and the continuous phospholipid remodeling that occurs while these molecules are in membranes. Oxidized PCs can be synthesized via three different routes. In one route, the oxidized PC is synthetized de novo following the same mechanisms as for PCs but incorporating oxidized acyl chains (PMID: 33329396 ). An alternative is the transacylation of one of the non-oxidated acyl chains with an oxidated acylCoA (PMID: 33329396 ). The third pathway results from the oxidation of the acyl chain while still attached to the PC backbone, mainely through the action of LOX (PMID: 33329396 ).
Structure
Thumb
SynonymsNot Available
Chemical FormulaC46H82NO10P
Average Molecular Weight840.133
Monoisotopic Molecular Weight839.567634842
IUPAC Name(2-{[(2R)-2-{[(5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoyl]oxy}-3-[(9Z)-octadeca-1,9-dien-1-yloxy]propyl phosphono]oxy}ethyl)trimethylazanium
Traditional Name(2-{[(2R)-2-{[(5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoyl]oxy}-3-[(9Z)-octadeca-1,9-dien-1-yloxy]propyl phosphono]oxy}ethyl)trimethylazanium
CAS Registry NumberNot Available
SMILES
CCCCCCCC\C=C/CCCCCCC=COC[C@H](COP([O-])(=O)OCC[N+](C)(C)C)OC(=O)CCC\C=C/C[C@H]1[C@@H](O)CC(=O)[C@@H]1\C=C\[C@@H](O)CCCCC
InChI Identifier
InChI=1S/C46H82NO10P/c1-6-8-10-11-12-13-14-15-16-17-18-19-20-21-24-28-35-54-38-41(39-56-58(52,53)55-36-34-47(3,4)5)57-46(51)31-27-23-22-26-30-42-43(45(50)37-44(42)49)33-32-40(48)29-25-9-7-2/h15-16,22,26,28,32-33,35,40-44,48-49H,6-14,17-21,23-25,27,29-31,34,36-39H2,1-5H3/b16-15-,26-22-,33-32+,35-28?/t40-,41+,42+,43+,44-/m0/s1
InChI KeyPWODTUOVVNIKHM-ISMNBZBVSA-N
Chemical Taxonomy
ClassificationNot classified
Ontology
Physiological effect
Disposition
Process
Role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP4.44ALOGPS
logP6ChemAxon
logS-7.2ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)-1.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area151.65 ŲChemAxon
Rotatable Bond Count38ChemAxon
Refractivity248.87 m³·mol⁻¹ChemAxon
Polarizability99.98 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+296.37932859911
AllCCS[M+H-H2O]+296.44832859911
AllCCS[M+Na]+296.25132859911
AllCCS[M+NH4]+296.28432859911
AllCCS[M-H]-285.84332859911
AllCCS[M+Na-2H]-290.73432859911
AllCCS[M+HCOO]-296.09632859911
DeepCCS[M+H]+281.94430932474
DeepCCS[M-H]-280.2730932474
DeepCCS[M-2H]-314.30230932474
DeepCCS[M+Na]+288.10130932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PC(P-18:1(9Z)/PGD2) 10V, Negative-QTOFsplash10-00di-0000000090-0e9fbfcb121b90bd13852021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PC(P-18:1(9Z)/PGD2) 20V, Negative-QTOFsplash10-00di-0000000090-0e9fbfcb121b90bd13852021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PC(P-18:1(9Z)/PGD2) 40V, Negative-QTOFsplash10-00di-0004920170-d52ebce775436c1f2a3e2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PC(P-18:1(9Z)/PGD2) 10V, Positive-QTOFsplash10-0006-0000000090-2b4b6b3c5c9c8b46a1482021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PC(P-18:1(9Z)/PGD2) 20V, Positive-QTOFsplash10-001l-0900000050-fa6838349d6a80513b932021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PC(P-18:1(9Z)/PGD2) 40V, Positive-QTOFsplash10-001l-1900141690-e3e666842fd377f32d0d2021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Hajeyah AA, Griffiths WJ, Wang Y, Finch AJ, O'Donnell VB: The Biosynthesis of Enzymatically Oxidized Lipids. Front Endocrinol (Lausanne). 2020 Nov 19;11:591819. doi: 10.3389/fendo.2020.591819. eCollection 2020. [PubMed:33329396 ]

Only showing the first 10 proteins. There are 72 proteins in total.

Enzymes

General function:
Involved in phospholipase A2 activity
Specific function:
PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. This isozyme hydrolyzes more efficiently L-alpha-1-palmitoyl-2-oleoyl phosphatidylcholine than L-alpha-1-palmitoyl-2-arachidonyl phosphatidylcholine, L-alpha-1-palmitoyl-2-arachidonyl phosphatidylethanolamine, or L-alpha-1-stearoyl-2-arachidonyl phosphatidylinositol. May be involved in the production of lung surfactant, the remodeling or regulation of cardiac muscle.
Gene Name:
PLA2G5
Uniprot ID:
P39877
Molecular weight:
15674.065
General function:
Involved in phospholipase A2 activity
Specific function:
PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. Hydrolyzes phosphatidylglycerol versus phosphatidylcholine with a 15-fold preference.
Gene Name:
PLA2G2F
Uniprot ID:
Q9BZM2
Molecular weight:
23256.29
General function:
Involved in metabolic process
Specific function:
Selectively hydrolyzes arachidonyl phospholipids in the sn-2 position releasing arachidonic acid. Together with its lysophospholipid activity, it is implicated in the initiation of the inflammatory response.
Gene Name:
PLA2G4A
Uniprot ID:
P47712
Molecular weight:
85210.19
General function:
Involved in phospholipase A2 activity
Specific function:
PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.
Gene Name:
PLA2G1B
Uniprot ID:
P04054
Molecular weight:
16359.535
General function:
Involved in phospholipase A2 activity
Specific function:
PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. Has a powerful potency for releasing arachidonic acid from cell membrane phospholipids. Prefers phosphatidylethanolamine and phosphatidylcholine liposomes to those of phosphatidylserine.
Gene Name:
PLA2G10
Uniprot ID:
O15496
Molecular weight:
18153.04
General function:
Involved in phospholipase A2 activity
Specific function:
PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. Has a preference for arachidonic-containing phospholipids.
Gene Name:
PLA2G2E
Uniprot ID:
Q9NZK7
Molecular weight:
15988.525
General function:
Involved in phospholipase A2 activity
Specific function:
PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. Does not exhibit detectable activity toward sn-2-arachidonoyl- or linoleoyl-phosphatidylcholine or -phosphatidylethanolamine.
Gene Name:
PLA2G12A
Uniprot ID:
Q9BZM1
Molecular weight:
21066.99
General function:
Involved in metabolic process
Specific function:
Catalyzes the release of fatty acids from phospholipids. It has been implicated in normal phospholipid remodeling, nitric oxide-induced or vasopressin-induced arachidonic acid release and in leukotriene and prostaglandin production. May participate in fas mediated apoptosis and in regulating transmembrane ion flux in glucose-stimulated B-cells. Has a role in cardiolipin (CL) deacylation. Required for both speed and directionality of monocyte MCP1/CCL2-induced chemotaxis through regulation of F-actin polymerization at the pseudopods. Isoform ankyrin-iPLA2-1 and isoform ankyrin-iPLA2-2, which lack the catalytic domain, are probably involved in the negative regulation of iPLA2 activity.
Gene Name:
PLA2G6
Uniprot ID:
O60733
Molecular weight:
84092.635
General function:
Involved in phosphatidylcholine-sterol O-acyltransferase activity
Specific function:
Central enzyme in the extracellular metabolism of plasma lipoproteins. Synthesized mainly in the liver and secreted into plasma where it converts cholesterol and phosphatidylcholines (lecithins) to cholesteryl esters and lysophosphatidylcholines on the surface of high and low density lipoproteins (HDLs and LDLs). The cholesterol ester is then transported back to the liver. Has a preference for plasma 16:0-18:2 or 18:O-18:2 phosphatidylcholines. Also produced in the brain by primary astrocytes, and esterifies free cholesterol on nascent APOE-containing lipoproteins secreted from glia and influences cerebral spinal fluid (CSF) APOE- and APOA1 levels. Together with APOE and the cholesterol transporter ABCA1, plays a key role in the maturation of glial-derived, nascent lipoproteins. Required for remodeling high-density lipoprotein particles into their spherical forms.
Gene Name:
LCAT
Uniprot ID:
P04180
Molecular weight:
49577.545
General function:
Involved in phospholipase A2 activity
Specific function:
Thought to participate in the regulation of the phospholipid metabolism in biomembranes including eicosanoid biosynthesis. Catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.
Gene Name:
PLA2G2A
Uniprot ID:
P14555
Molecular weight:
16082.525

Transporters

General function:
Involved in ATP binding
Specific function:
Mediates ATP-dependent export of organic anions and drugs from the cytoplasm. Hydrolyzes ATP with low efficiency. Human MDR3 is not capable of conferring drug resistance. Mediates the translocation of phosphatidylcholine across the canalicular membrane of the hepatocyte
Gene Name:
ABCB4
Uniprot ID:
P21439
Molecular weight:
141521.8

Only showing the first 10 proteins. There are 72 proteins in total.