Hmdb loader
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-09-09 06:32:07 UTC
Update Date2022-11-30 19:26:24 UTC
HMDB IDHMDB0115954
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z))
DescriptionCDP-DG(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)) is a cytidine diphosphate diacylglycerol or CDP-diacylglycerol (CDP-DG). CDP-diacylglycerol is an important branchpoint intermediate in eukaryotic phospholipid biosynthesis and could be a key regulatory molecule in phospholipid metabolism. It is a glycerophospholipid in which a cytidine diphosphate moiety occupies a glycerol substitution site. As is the case with diacylglycerols, CDP-diacylglycerols can have many different combinations of fatty acids of varying lengths and saturation attached at the C-1 and C-2 positions. Fatty acids containing 16, 18 and 20 carbons are the most common. CDP-DG(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)), in particular, consists of one chain of palmitoleic acid at the C-1 position and one chain of osbond acid at the C-2 position. Cytidine diphosphate diacylglycerols are rarely noticed in analyses of lipid compositions of tissues, as they are present is such small amounts (perhaps only 0.05% or so of the total phospholipids).
Structure
Data?1563873654
Synonyms
ValueSource
1-palmitoleoyl-2-osbondoyl-sn-glycero-3-CDP SMPDB, HMDB
1-palmitoleoyl-2-osbondoyl-sn-glycero-3-cytidine-5'-diphosphate SMPDB, HMDB
CDP-DG(16:1/22:5) SMPDB, HMDB
CDP-DG(16:1n7/22:5n6) SMPDB, HMDB
CDP-DG(16:1w7/22:5w6) SMPDB, HMDB
CDP-DG(38:6) SMPDB, HMDB
CDP-diacylglycerol(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)) SMPDB, HMDB
CDP-diacylglycerol(16:1/22:5) SMPDB, HMDB
CDP-diacylglycerol(16:1n7/22:5n6) SMPDB, HMDB
CDP-diacylglycerol(16:1w7/22:5w6) SMPDB, HMDB
CDP-diacylglycerol(38:6)SMPDB, HMDB
CDP-DG(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z))SMPDB
{[(2R,3R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({[(2R)-2-[(4Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoyloxy]-3-[(9Z)-hexadec-9-enoyloxy]propoxy](hydroxy)phosphoryl}oxy)phosphinateGenerator, HMDB
Chemical FormulaC50H81N3O15P2
Average Molecular Weight1026.152
Monoisotopic Molecular Weight1025.514292916
IUPAC Name{[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[(2R)-2-[(4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoyloxy]-3-[(9Z)-hexadec-9-enoyloxy]propoxy](hydroxy)phosphoryl}oxy)phosphinic acid
Traditional Name[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([(2R)-2-[(4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoyloxy]-3-[(9Z)-hexadec-9-enoyloxy]propoxy(hydroxy)phosphoryl]oxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](COC(=O)CCCCCCC\C=C/CCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CC\C=C/C\C=C/C\C=C/C\C=C/C\C=C/CCCCC
InChI Identifier
InChI=1S/C50H81N3O15P2/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-24-26-28-30-32-34-36-46(55)66-42(39-63-45(54)35-33-31-29-27-25-23-16-14-12-10-8-6-4-2)40-64-69(59,60)68-70(61,62)65-41-43-47(56)48(57)49(67-43)53-38-37-44(51)52-50(53)58/h11,13-14,16-18,20-21,24,26,30,32,37-38,42-43,47-49,56-57H,3-10,12,15,19,22-23,25,27-29,31,33-36,39-41H2,1-2H3,(H,59,60)(H,61,62)(H2,51,52,58)/b13-11-,16-14-,18-17-,21-20-,26-24-,32-30-/t42-,43-,47+,48?,49-/m1/s1
InChI KeyIZWMZNIXBJLGEE-FOQJXRGESA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cdp-diacylglycerols. These are glycerolipids containing a diacylglycerol, with a cytidine diphosphate attached to the oxygen O1 or O2 of the glycerol part.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassGlycerophospholipids
Sub ClassCDP-glycerols
Direct ParentCDP-diacylglycerols
Alternative Parents
Substituents
  • Cdp-diacylglycerol
  • Pyrimidine ribonucleoside diphosphate
  • Diacyl-glycerol-3-pyrophosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Pentose monosaccharide
  • Aminopyrimidine
  • Fatty acid ester
  • Pyrimidone
  • Monoalkyl phosphate
  • Imidolactam
  • Pyrimidine
  • Fatty acyl
  • Alkyl phosphate
  • Phosphoric acid ester
  • Dicarboxylic acid or derivatives
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Monosaccharide
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Secondary alcohol
  • Amino acid or derivatives
  • 1,2-diol
  • Carboxylic acid ester
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Carboxylic acid derivative
  • Alcohol
  • Organonitrogen compound
  • Organic nitrogen compound
  • Organooxygen compound
  • Amine
  • Carbonyl group
  • Primary amine
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
DispositionNot Available
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
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
logP7.01ALOGPS
logP10.05ChemAxon
logS-5.8ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)-0.032ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area263.27 ŲChemAxon
Rotatable Bond Count42ChemAxon
Refractivity274.52 m³·mol⁻¹ChemAxon
Polarizability110.12 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
DeepCCS[M+H]+283.85230932474
DeepCCS[M-H]-282.02730932474
DeepCCS[M-2H]-315.5330932474
DeepCCS[M+Na]+289.45830932474
AllCCS[M+H]+316.632859911
AllCCS[M+H-H2O]+316.932859911
AllCCS[M+NH4]+316.232859911
AllCCS[M+Na]+316.132859911
AllCCS[M-H]-298.432859911
AllCCS[M+Na-2H]-305.432859911
AllCCS[M+HCOO]-313.132859911

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - CDP-DG(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)) GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-13Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 10V, Positive-QTOFsplash10-03di-1911001000-94621c22c5d47e1be8b52019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 20V, Positive-QTOFsplash10-03di-2911000100-eaa62a94f3735f05feac2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 40V, Positive-QTOFsplash10-03di-3921000000-644c0d57b20f91627acc2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 10V, Negative-QTOFsplash10-0np0-2893001202-04d3d49753ac102490202019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 20V, Negative-QTOFsplash10-0w30-7793210200-da3b51013a35101bd52e2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 40V, Negative-QTOFsplash10-0bvi-5911000000-6a3f212cbb49de14015f2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 10V, Positive-QTOFsplash10-004i-9100000024-e411e425010061c2c6752021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 20V, Positive-QTOFsplash10-06vi-3100000019-ef73820aa6dbf0725c532021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 40V, Positive-QTOFsplash10-0fdx-1288900000-bf1f92187d9f90ad1cc12021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 10V, Negative-QTOFsplash10-00di-9001003000-aea231155fb77fd2a74d2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 20V, Negative-QTOFsplash10-0fbl-9083702100-a895cdced04dc9c25b2e2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)) 40V, Negative-QTOFsplash10-0a4i-9228400400-d809172cc94e00c5d2792021-09-23Wishart 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 Compound131822610
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 ReferencesNot Available