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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-17 12:49:05 UTC
Update Date2022-11-30 20:08:28 UTC
HMDB IDHMDB0293195
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(a-25:0/20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S))
DescriptionCDP-DG(a-25:0/20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)) 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(a-25:0/20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)), in particular, consists of one chain of one 22-methyltetracosanoyl at the C-1 position and one chain of Lipoxin A4 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
{[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({hydroxy[(2R)-3-[(22-methyltetracosanoyl)oxy]-2-{[(5S,6S,7E,9E,11Z,15S)-5,6,15-trihydroxyicosa-7,9,11,13-tetraenoyl]oxy}propoxy]phosphoryl}oxy)phosphinateGenerator
Chemical FormulaC57H99N3O18P2
Average Molecular Weight1176.37
Monoisotopic Molecular Weight1175.639887356
IUPAC Name{[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(2R)-3-[(22-methyltetracosanoyl)oxy]-2-{[(5S,6S,7E,9E,11Z,13E,15S)-5,6,15-trihydroxyicosa-7,9,11,13-tetraenoyl]oxy}propoxy]phosphoryl}oxy)phosphinic acid
Traditional Name[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([hydroxy((2R)-3-[(22-methyltetracosanoyl)oxy]-2-{[(5S,6S,7E,9E,11Z,13E,15S)-5,6,15-trihydroxyicosa-7,9,11,13-tetraenoyl]oxy}propoxy)phosphoryl]oxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](COC(=O)CCCCCCCCCCCCCCCCCCCCC(C)CC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCC[C@H](O)[C@@H](O)\C=C\C=C\C=C/C=C/[C@@H](O)CCCCC
InChI Identifier
InChI=1S/C57H99N3O18P2/c1-4-6-27-34-46(61)35-29-24-21-22-25-30-36-48(62)49(63)37-32-39-53(65)76-47(42-73-52(64)38-31-26-20-18-16-14-12-10-8-7-9-11-13-15-17-19-23-28-33-45(3)5-2)43-74-79(69,70)78-80(71,72)75-44-50-54(66)55(67)56(77-50)60-41-40-51(58)59-57(60)68/h21-22,24-25,29-30,35-36,40-41,45-50,54-56,61-63,66-67H,4-20,23,26-28,31-34,37-39,42-44H2,1-3H3,(H,69,70)(H,71,72)(H2,58,59,68)/b24-21-,25-22+,35-29+,36-30+/t45?,46-,47+,48-,49-,50+,54+,55+,56+/m0/s1
InChI KeyYNNIEWYGQBDQGT-MGMIRCLXSA-N
Chemical Taxonomy
ClassificationNot classified
Ontology
Physiological effectNot Available
Disposition
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
logP6.8ALOGPS
logP10.19ChemAxon
logS-5.8ALOGPS
pKa (Strongest Acidic)-0.02ChemAxon
pKa (Strongest Basic)3.27ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area323.96 ŲChemAxon
Rotatable Bond Count50ChemAxon
Refractivity308.83 m³·mol⁻¹ChemAxon
Polarizability131.35 ųChemAxon
Number of Rings2ChemAxon
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]+339.73232859911
AllCCS[M+H-H2O]+340.08732859911
AllCCS[M+Na]+339.27332859911
AllCCS[M+NH4]+339.37932859911
AllCCS[M-H]-309.01632859911
AllCCS[M+Na-2H]-314.42832859911
AllCCS[M+HCOO]-320.25932859911
DeepCCS[M+H]+316.88230932474
DeepCCS[M-H]-315.15830932474
DeepCCS[M-2H]-349.19230932474
DeepCCS[M+Na]+323.11830932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. 8.16 minutes32390414
Predicted by Siyang on May 30, 202225.4062 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.44 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid5195.6 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid126.2 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid359.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid195.2 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid912.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1439.1 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid1198.0 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)405.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid2611.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid1265.3 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid2412.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid976.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid719.9 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate120.7 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA121.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water10.4 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra
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 ]