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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-12 21:40:30 UTC
Update Date2022-11-30 19:58:56 UTC
HMDB IDHMDB0272491
Secondary Accession NumbersNone
Metabolite Identification
Common NamePGP(PGD1/16:1(9Z))
DescriptionPGP(PGD1/16:1(9Z)) is an oxidized phosphoglycerophosphate (PGP). Oxidized phosphoglycerophosphates are glycerophospholipids in which a phosphoglycerol moiety occupies a glycerol substitution site and at least one of the fatty acyl chains has undergone oxidation. As all oxidized lipids, oxidized phosphoglycerophosphates 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, phosphoglycerophosphates 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. PGP(PGD1/16:1(9Z)), in particular, consists of one chain of one Prostaglandin D1 at the C-1 position and one chain of 9Z-hexadecenoyl 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 PGPs can be synthesized via three different routes. In one route, the oxidized PGP is synthetized de novo following the same mechanisms as for PGPs but incorporating oxidized acyl chains (PMID: 33329396 ). An alternative is the transacylation of one of the non-oxidized acyl chains with an oxidized acylCoA (PMID: 33329396 ). The third pathway results from the oxidation of the acyl chain while still attached to the PGP backbone, mainely through the action of LOX (PMID: 33329396 ).
Structure
Thumb
Synonyms
ValueSource
[(2S)-3-({[(2R)-2-[(9Z)-hexadec-9-enoyloxy]-3-({7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]heptanoyl}oxy)propoxy](hydroxy)phosphoryl}oxy)-2-hydroxypropoxy]phosphonateGenerator
Chemical FormulaC42H76O16P2
Average Molecular Weight899.002
Monoisotopic Molecular Weight898.460860363
IUPAC Name[(2S)-3-({[(2R)-2-[(9Z)-hexadec-9-enoyloxy]-3-({7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]heptanoyl}oxy)propoxy](hydroxy)phosphoryl}oxy)-2-hydroxypropoxy]phosphonic acid
Traditional Name(2S)-3-{[(2R)-2-[(9Z)-hexadec-9-enoyloxy]-3-({7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]heptanoyl}oxy)propoxy(hydroxy)phosphoryl]oxy}-2-hydroxypropoxyphosphonic acid
CAS Registry NumberNot Available
SMILES
CCCCCC\C=C/CCCCCCCC(=O)O[C@H](COC(=O)CCCCCC[C@H]1[C@@H](O)CC(=O)[C@@H]1\C=C\[C@@H](O)CCCCC)COP(O)(=O)OC[C@@H](O)COP(O)(O)=O
InChI Identifier
InChI=1S/C42H76O16P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-22-26-42(48)58-36(33-57-60(52,53)56-31-35(44)30-55-59(49,50)51)32-54-41(47)25-21-18-17-20-24-37-38(40(46)29-39(37)45)28-27-34(43)23-19-6-4-2/h10-11,27-28,34-39,43-45H,3-9,12-26,29-33H2,1-2H3,(H,52,53)(H2,49,50,51)/b11-10-,28-27+/t34-,35-,36+,37+,38+,39-/m0/s1
InChI KeyFVYQZUMYHUHDCT-TZONCCGGSA-N
Chemical Taxonomy
ClassificationNot classified
Ontology
Physiological effectNot Available
DispositionNot Available
ProcessNot Available
RoleNot Available
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
logP4.72ALOGPS
logP7.78ChemAxon
logS-5.7ALOGPS
pKa (Strongest Acidic)1.36ChemAxon
pKa (Strongest Basic)-1.6ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area252.88 ŲChemAxon
Rotatable Bond Count40ChemAxon
Refractivity228.53 m³·mol⁻¹ChemAxon
Polarizability96.5 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]+297.27632859911
AllCCS[M+H-H2O]+297.60232859911
AllCCS[M+Na]+296.8332859911
AllCCS[M+NH4]+296.93532859911
AllCCS[M-H]-293.75332859911
AllCCS[M+Na-2H]-300.15532859911
AllCCS[M+HCOO]-307.1832859911
DeepCCS[M+H]+312.72930932474
DeepCCS[M-H]-311.00630932474
DeepCCS[M-2H]-345.0430932474
DeepCCS[M+Na]+319.05830932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PGP(PGD1/16:1(9Z))CCCCCC\C=C/CCCCCCCC(=O)O[C@H](COC(=O)CCCCCC[C@H]1[C@@H](O)CC(=O)[C@@H]1\C=C\[C@@H](O)CCCCC)COP(O)(=O)OC[C@@H](O)COP(O)(O)=O5538.5Standard polar33892256
PGP(PGD1/16:1(9Z))CCCCCC\C=C/CCCCCCCC(=O)O[C@H](COC(=O)CCCCCC[C@H]1[C@@H](O)CC(=O)[C@@H]1\C=C\[C@@H](O)CCCCC)COP(O)(=O)OC[C@@H](O)COP(O)(O)=O4930.1Standard non polar33892256
PGP(PGD1/16:1(9Z))CCCCCC\C=C/CCCCCCCC(=O)O[C@H](COC(=O)CCCCCC[C@H]1[C@@H](O)CC(=O)[C@@H]1\C=C\[C@@H](O)CCCCC)COP(O)(=O)OC[C@@H](O)COP(O)(O)=O6308.4Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(PGD1/16:1(9Z)) 10V, Positive-QTOFsplash10-03e9-0000003290-087d4aad4e5f5533bc732021-10-18Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(PGD1/16:1(9Z)) 20V, Positive-QTOFsplash10-001i-2110003950-e65ef7918b7c8eb4d73c2021-10-18Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(PGD1/16:1(9Z)) 40V, Positive-QTOFsplash10-052f-7906703200-2cbfaa9e70d98999e4a22021-10-18Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(PGD1/16:1(9Z)) 10V, Negative-QTOFsplash10-004i-0000000090-f8ea8b219cf2470a514b2021-10-18Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(PGD1/16:1(9Z)) 20V, Negative-QTOFsplash10-004i-9022015250-1f05e79220cfd631f05d2021-10-18Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(PGD1/16:1(9Z)) 40V, Negative-QTOFsplash10-004i-9034001000-fad133b7ca9f09f29db42021-10-18Wishart 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 ]