Identification
YMDB IDYMDB12507
NameCDP-DG(20:0/28:1(11Z))
SpeciesSaccharomyces cerevisiae
StrainBrewer's yeast
DescriptionCDP-DG(20:0/28:1(11Z)) belongs to the family of CDP-diacylglycerols. It is a glycerophospholipid containing a diacylglycerol, with a cytidine diphosphate attached to the oxygen O1 or O2 of the glycerol part. As is the case with diacylglycerols, phosphatidylserines can have many different combinations of fatty acids of varying lengths and saturation attached to the C-1 and C-2 positions. CDP-DG(20:0/28:1(11Z)), in particular, consists of two eicosanoyl chain at positions C-1 and C2. In E. coli glycerophospholipid metabolism, The biosynthesis of CDP-diacylglycerol (CDP-DG) involves condensation of phosphatidic acid (PA) and cytidine triphosphate, with elimination of pyrophosphate, catalysed by the enzyme CDP-diacylglycerol synthase. The resulting CDP-diacylglycerol can be utilized immediately for the synthesis of phosphatidylglycerol (PG), and thence cardiolipin (CL), and of phosphatidylinositol (PI). CDP-DG(20:0/28:1(11Z)) is also a substrate of CDP-diacylglycerol pyrophosphatase. It is involved in CDP-diacylglycerol degradation pathway.
Structure
Thumb
SynonymsNot Available
CAS numberNot Available
WeightAverage: 1176.502
Monoisotopic: 1175.749043882
InChI KeyVZJCJVGNLSTDMT-OEIFJQQOSA-N
InChIInChI=1S/C60H111N3O15P2/c1-3-5-7-9-11-13-15-17-19-21-22-23-24-25-26-27-28-30-32-34-36-38-40-42-44-46-56(65)76-52(49-73-55(64)45-43-41-39-37-35-33-31-29-20-18-16-14-12-10-8-6-4-2)50-74-79(69,70)78-80(71,72)75-51-53-57(66)58(67)59(77-53)63-48-47-54(61)62-60(63)68/h26-27,47-48,52-53,57-59,66-67H,3-25,28-46,49-51H2,1-2H3,(H,69,70)(H,71,72)(H2,61,62,68)/b27-26-/t52-,53-,57+,58?,59-/m1/s1
IUPAC Name{[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(2R)-3-(icosanoyloxy)-2-[(12Z)-octacos-12-enoyloxy]propoxy]phosphoryl}oxy)phosphinic acid
Traditional IUPAC Name[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([hydroxy((2R)-3-(icosanoyloxy)-2-[(12Z)-octacos-12-enoyloxy]propoxy)phosphoryl]oxy)phosphinic acid
Chemical FormulaC60H111N3O15P2
SMILES[H][C@@](COC(=O)CCCCCCCCCCCCCCCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCCC\C=C/CCCCCCCCCCCCCCC
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-5-phosphate
  • Pentose phosphate
  • N-glycosyl compound
  • Glycosyl compound
  • Pentose monosaccharide
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Pyrimidone
  • Fatty acid ester
  • Aminopyrimidine
  • Fatty acyl
  • Imidolactam
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Monosaccharide
  • Hydropyrimidine
  • Dicarboxylic acid or derivatives
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Carboxylic acid ester
  • Amino acid or derivatives
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Amine
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.00034 g/LALOGPS
logP8.62ALOGPS
logP16.31ChemAxon
logS-6.5ALOGPS
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 Count57ChemAxon
Refractivity314.94 m³·mol⁻¹ChemAxon
Polarizability137.48 ųChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • Mitochondrion membrane
Organoleptic PropertiesNot Available
SMPDB Pathways
Cardiolipin Biosynthesis CL(12:0/12:0/20:0/28:1(11Z))PW006064 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG PathwaysNot Available
SMPDB Reactions
PG(10:0/10:0) + CDP-DG(20:0/28:1(11Z))Cytidine monophosphate + hydron + CL(16:0/16:0/16:0/16:0)
PG(16:0/16:0) + CDP-DG(20:0/28:1(11Z))Cytidine monophosphate + hydron + CL(16:0/16:0/16:0/16:0)
PG(10:0/10:0) + CDP-DG(20:0/28:1(11Z))Cytidine monophosphate + hydron + CL(10:0/10:0/20:0/28:1(11Z))
PG(16:0/16:0) + CDP-DG(20:0/28:1(11Z))Cytidine monophosphate + hydron + CL(10:0/12:0/20:0/28:1(11Z))
PG(16:0/16:0) + CDP-DG(20:0/28:1(11Z))Cytidine monophosphate + hydron + CL(10:0/14:0/20:0/28:1(11Z))
KEGG ReactionsNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0910000100-8455d5f7352851319c28JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1910000000-b4f5489a85ea25caf405JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-3912000000-170b78da3fc08d63dc32JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-08ml-0923200100-c2a0ac02be21d36d42d6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03di-6937301002-f0b1ff9ef22d719f868aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0bvi-5902000000-2da68e041c190f07ec00JSpectraViewer
References
References:
  • Rattray JB, Schibeci A, Kidby DK. (1975). "Lipids of yeasts." Bacteriol Rev. 1975 Sep;39(3):197-231.240350
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound IDNot Available
Kegg IDNot Available
ChemSpider IDNot Available
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

General function:
Involved in phosphotransferase activity, for other substituted phosphate groups
Specific function:
Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol
Gene Name:
CRD1
Uniprot ID:
Q07560
Molecular weight:
32019.30078
Reactions
2 Phosphatidylglycerol → diphosphatidylglycerol + glycerol.