CDP-DG(20:0/24:0) (YMDB12494)

Identification
YMDB IDYMDB12494
NameCDP-DG(20:0/24:0)
SpeciesSaccharomyces cerevisiae
StrainBrewer's yeast
DescriptionCDP-DG(20:0/24:0) 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(20:0/24:0), 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(20:0/24:0) 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: 1122.41
Monoisotopic: 1121.702093689
InChI KeyPJQJEBLJAVXSMW-CKZKIYGOSA-N
InChIInChI=1S/C56H105N3O15P2/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/h43-44,48-49,53-55,62-63H,3-42,45-47H2,1-2H3,(H,65,66)(H,67,68)(H2,57,58,64)/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-(tetracosanoyloxy)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-(tetracosanoyloxy)propoxy)phosphoryl]oxy)phosphinic acid
Chemical FormulaC56H105N3O15P2
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)CCCCCCCCCCCCCCCCCCCCCCC
Chemical Taxonomy
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.00052 g/LALOGPS
logP8.14ALOGPS
logP14.89ChemAxon
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 Count54ChemAxon
Refractivity295.42 m³·mol⁻¹ChemAxon
Polarizability130.44 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(10:0/16:0/20:0/24:0)PW005279 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/16:1(11Z)/20:0/24:0)PW005423 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/16:1(9Z)/20:0/24:0)PW005567 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/18:0/20:0/24:0)PW005664 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/18:1(11Z)/20:0/24:0)PW005724 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG PathwaysNot Available
SMPDB Reactions
PG(10:0/10:0) + CDP-DG(20:0/24:0) → Cytidine monophosphate + hydron + CL(16:0/16:0/16:0/16:0)
PG(16:0/16:0) + CDP-DG(20:0/24:0) → Cytidine monophosphate + hydron + CL(16:0/16:0/16:0/16:0)
PG(10:0/10:0) + CDP-DG(20:0/24:0) → Cytidine monophosphate + hydron + CL(10:0/10:0/20:0/24:0)
PG(16:0/16:0) + CDP-DG(20:0/24:0) → Cytidine monophosphate + hydron + CL(10:0/12:0/20:0/24:0)
PG(16:0/16:0) + CDP-DG(20:0/24:0) → Cytidine monophosphate + hydron + CL(10:0/14:0/20:0/24:0)
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-c467c9e7f4c86f1db3d7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1911000110-dfe8baf85bec4449d932JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-3912000000-735d9a831c2d88ccba76JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-08fu-1936000110-f0e10ebfc08f3e26bb3fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03di-5839110020-d6806c5fd120c7204c98JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0bvi-5903000000-c74898811907e5388c14JSpectraViewer
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.