CDP-DG(20:0/24:1(9Z)) (YMDB12496)

Identification
YMDB IDYMDB12496
NameCDP-DG(20:0/24:1(9Z))
SpeciesSaccharomyces cerevisiae
StrainBrewer's yeast
DescriptionCDP-DG(20:0/24:1(9Z)) 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(20:0/24:1(9Z)), 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(20:0/24:1(9Z)) is also a substrate of CDP-diacylglycerol pyrophosphatase. It is involved in CDP-diacylglycerol degradation pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
SynonymsNot Available
CAS numberNot Available
WeightAverage: 1120.394
Monoisotopic: 1119.686443625
InChI KeyGEUIQJLEPFBOSX-KHXPFIJUSA-N
InChIInChI=1S/C56H103N3O15P2/c1-3-5-7-9-11-13-15-17-19-21-22-23-24-26-28-30-32-34-36-38-40-42-52(61)72-48(45-69-51(60)41-39-37-35-33-31-29-27-25-20-18-16-14-12-10-8-6-4-2)46-70-75(65,66)74-76(67,68)71-47-49-53(62)54(63)55(73-49)59-44-43-50(57)58-56(59)64/h26,28,43-44,48-49,53-55,62-63H,3-25,27,29-42,45-47H2,1-2H3,(H,65,66)(H,67,68)(H2,57,58,64)/b28-26-/t48-,49-,53+,54?,55-/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-[(9Z)-tetracos-9-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-[(9Z)-tetracos-9-enoyloxy]propoxy)phosphoryl]oxy)phosphinic acid
Chemical FormulaC56H103N3O15P2
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)CCCCCCC\C=C/CCCCCCCCCCCCCC
Chemical Taxonomy
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.00055 g/LALOGPS
logP8.19ALOGPS
logP14.53ChemAxon
logS-6.3ALOGPS
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 Count53ChemAxon
Refractivity296.54 m³·mol⁻¹ChemAxon
Polarizability128.97 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(10:0/10:0/20:0/24:1(9Z))PW003628 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/12:0/20:0/24:1(9Z))PW003904 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/14:0/20:0/24:1(9Z))PW004194 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/14:1(11Z)/20:0/24:1(9Z))PW004435 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/14:1(9Z)/20:0/24:1(9Z))PW004676 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG PathwaysNot Available
SMPDB Reactions
PG(10:0/10:0) + CDP-DG(20:0/24:1(9Z)) → Cytidine monophosphate + hydron + CL(16:0/16:0/16:0/16:0)
PG(16:0/16:0) + CDP-DG(20:0/24:1(9Z)) → Cytidine monophosphate + hydron + CL(16:0/16:0/16:0/16:0)
PG(10:0/10:0) + CDP-DG(20:0/24:1(9Z)) → Cytidine monophosphate + hydron + CL(10:0/10:0/20:0/24:1(9Z))
PG(16:0/16:0) + CDP-DG(20:0/24:1(9Z)) → Cytidine monophosphate + hydron + CL(10:0/12:0/20:0/24:1(9Z))
PG(16:0/16:0) + CDP-DG(20:0/24:1(9Z)) → Cytidine monophosphate + hydron + CL(10:0/14:0/20:0/24:1(9Z))
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-0911000100-2cc86a27554ce3a92fe6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1911000100-101e9d4dfa374521dfacJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-3912000000-90bdb461a64126782b1fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0903-1936000110-d04d4b082022737273acJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03di-5839110020-300cedff18ce041b3d28JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0bvi-5903000000-74d979ce83cb1aa880c6JSpectraViewer
MSMass Spectrum (Electron Ionization)Not AvailableJSpectraViewer
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

Protein Details
1. Cardiolipin synthase
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.