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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-17 10:37:00 UTC
Update Date2022-11-30 20:08:20 UTC
HMDB IDHMDB0292888
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(5-iso PGF2VI/a-15:0)
DescriptionCDP-DG(5-iso PGF2VI/a-15:0) is an oxidized CDP-diacylglycerol (CDP-DG). Oxidized CDP-diacylglycerols are glycerophospholipids in which a cytidine diphosphate moiety occupies a glycerol substitution site and at least one of the fatty acyl chains has undergone oxidation. As all oxidized lipids, oxidized CDP-diacylglycerols 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, CDP-diacylglycerols 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. CDP-DG(5-iso PGF2VI/a-15:0), in particular, consists of one chain of one 5-iso Prostaglandin F2alpha-VI at the C-1 position and one chain of 12-methyltetradecanoyl 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 CDP-DGs can be synthesized via three different routes. In one route, the oxidized CDP-DG is synthetized de novo following the same mechanisms as for CDP-DGs 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 CDP-DG backbone, mainly through the action of LOX (PMID: 33329396 ).
Structure
Thumb
Synonyms
ValueSource
(1R,9R,14Z,17R,21S,22S,23S,25R)-4,6,18,20,22,23-Hexahydroxy-25-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-21-[(3R)-3-hydroxyoct-1-en-1-yl]-4,6,12-trioxo-3,5,7,11,24-pentaoxa-4,6-diphosphabicyclo[15.6.2]pentacos-14-en-9-yl 12-methyltetradecanoic acidGenerator
Chemical FormulaC45H77N3O18P2
Average Molecular Weight1010.062
Monoisotopic Molecular Weight1009.467736647
IUPAC Name(1R,9R,14Z,17R,18S,20R,21S,22S,23S,25R)-25-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-4,6,18,20,22,23-hexahydroxy-21-[(1E,3R)-3-hydroxyoct-1-en-1-yl]-4,6,12-trioxo-3,5,7,11,24-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[15.6.2]pentacos-14-en-9-yl 12-methyltetradecanoate
Traditional Name(1R,9R,14Z,17R,18S,20R,21S,22S,23S,25R)-25-(4-amino-2-oxopyrimidin-1-yl)-4,6,18,20,22,23-hexahydroxy-21-[(1E,3R)-3-hydroxyoct-1-en-1-yl]-4,6,12-trioxo-3,5,7,11,24-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[15.6.2]pentacos-14-en-9-yl 12-methyltetradecanoate
CAS Registry NumberNot Available
SMILES
CCCCC[C@@H](O)C=C[C@H]1[C@H](O)C[C@H](O)[C@H]2C\C=C/CC(=O)OC[C@H](COP(O)(=O)OP(O)(=O)OC[C@@H](O[C@H]2N2C=CC(N)=NC2=O)[C@@H](O)[C@H]1O)OC(=O)CCCCCCCCCCC(C)CC
InChI Identifier
InChI=1S/C45H77N3O18P2/c1-4-6-13-19-32(49)23-24-34-36(50)27-37(51)35-20-16-17-21-40(52)61-28-33(64-41(53)22-15-12-10-8-7-9-11-14-18-31(3)5-2)29-62-67(57,58)66-68(59,60)63-30-38(43(55)42(34)54)65-44(35)48-26-25-39(46)47-45(48)56/h16-17,23-26,31-38,42-44,49-51,54-55H,4-15,18-22,27-30H2,1-3H3,(H,57,58)(H,59,60)(H2,46,47,56)/b17-16-,24-23?/t31?,32-,33-,34+,35-,36?,37?,38-,42+,43-,44-/m1/s1
InChI KeyXUWMNXGEYHAJBL-LXTDWMIVSA-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
logP2.54ALOGPS
logP4.17ChemAxon
logS-3.5ALOGPS
pKa (Strongest Acidic)0.27ChemAxon
pKa (Strongest Basic)3.27ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area323.96 ŲChemAxon
Rotatable Bond Count21ChemAxon
Refractivity249.65 m³·mol⁻¹ChemAxon
Polarizability103.81 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+300.83932859911
AllCCS[M+H-H2O]+301.29232859911
AllCCS[M+Na]+300.24432859911
AllCCS[M+NH4]+300.38232859911
AllCCS[M-H]-306.1132859911
AllCCS[M+Na-2H]-312.56332859911
AllCCS[M+HCOO]-319.60632859911
DeepCCS[M+H]+255.08330932474
DeepCCS[M-H]-253.4330932474
DeepCCS[M-2H]-288.38830932474
DeepCCS[M+Na]+261.65130932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(5-iso PGF2VI/a-15:0) 10V, Positive-QTOFsplash10-03kc-6500000009-d688445864cb19e1f0962021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(5-iso PGF2VI/a-15:0) 20V, Positive-QTOFsplash10-0abc-9100000025-45c5664650da1a4ebb242021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(5-iso PGF2VI/a-15:0) 40V, Positive-QTOFsplash10-0aor-9400001500-6a4c3a14dfefe6690c762021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(5-iso PGF2VI/a-15:0) 10V, Negative-QTOFsplash10-0a4i-9000000003-6db3f55154f24ad2bd2f2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(5-iso PGF2VI/a-15:0) 20V, Negative-QTOFsplash10-06xx-4220000229-3eab8c53a99dc0882c292021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(5-iso PGF2VI/a-15:0) 40V, Negative-QTOFsplash10-03xu-7910002724-120a4b47cada109ea7102021-10-21Wishart 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 ]