CDP-DG(18:1(9Z)/25:1(11Z)) (YMDB12473)

Identification
YMDB IDYMDB12473
NameCDP-DG(18:1(9Z)/25:1(11Z))
SpeciesSaccharomyces cerevisiae
StrainBrewer's yeast
DescriptionCDP-DG(18:1(9Z)/25:1(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(18:1(9Z)/25:1(11Z)), in particular, consists of two 9Z-octadecenoyl 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(18:1(9Z)/25:1(11Z)) 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: 1104.351
Monoisotopic: 1103.655143496
InChI KeyBDLHVESUANWGTP-WGROYRRMSA-N
InChIInChI=1S/C55H99N3O15P2/c1-3-5-7-9-11-13-15-17-19-20-21-22-23-24-25-27-29-31-33-35-37-39-41-51(60)71-47(44-68-50(59)40-38-36-34-32-30-28-26-18-16-14-12-10-8-6-4-2)45-69-74(64,65)73-75(66,67)70-46-48-52(61)53(62)54(72-48)58-43-42-49(56)57-55(58)63/h18,23-24,26,42-43,47-48,52-54,61-62H,3-17,19-22,25,27-41,44-46H2,1-2H3,(H,64,65)(H,66,67)(H2,56,57,63)/b24-23-,26-18-/t47-,48-,52+,53?,54-/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-[(9Z)-octadec-9-enoyloxy]-2-[(11Z)-pentacos-11-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-[(9Z)-octadec-9-enoyloxy]-2-[(11Z)-pentacos-11-enoyloxy]propoxy)phosphoryl]oxy)phosphinic acid
Chemical FormulaC55H99N3O15P2
SMILES[H][C@@](COC(=O)CCCCCCC\C=C/CCCCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCC\C=C/CCCCCCCCCCCCC
Chemical Taxonomy
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.00074 g/LALOGPS
logP8.01ALOGPS
logP13.72ChemAxon
logS-6.2ALOGPS
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 Count51ChemAxon
Refractivity293.05 m³·mol⁻¹ChemAxon
Polarizability124.34 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(10:0/15:0/18:1(9Z)/25:1(11Z))PW004850 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/15:1(11Z)/18:1(9Z)/25:1(11Z))PW004981 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/15:1(9Z)/18:1(9Z)/25:1(11Z))PW005112 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(12:0/15:0/18:1(9Z)/25:1(11Z))PW006906 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(12:0/15:1(11Z)/18:1(9Z)/25:1(11Z))PW007016 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG PathwaysNot Available
SMPDB Reactions
PG(16:0/16:0) + CDP-DG(18:1(9Z)/25:1(11Z)) → Cytidine monophosphate + hydron + CL(10:0/15:0/18:1(9Z)/25:1(11Z))
PG(16:0/16:0) + CDP-DG(18:1(9Z)/25:1(11Z)) → Cytidine monophosphate + hydron + CL(10:0/15:1(11Z)/18:1(9Z)/25:1(11Z))
PG(16:0/16:0) + CDP-DG(18:1(9Z)/25:1(11Z)) → Cytidine monophosphate + hydron + CL(10:0/15:1(9Z)/18:1(9Z)/25:1(11Z))
PG(16:0/16:0) + CDP-DG(18:1(9Z)/25:1(11Z)) → Cytidine monophosphate + hydron + CL(12:0/15:0/18:1(9Z)/25:1(11Z))
PG(16:0/16:0) + CDP-DG(18:1(9Z)/25:1(11Z)) → Cytidine monophosphate + hydron + CL(12:0/15:1(11Z)/18:1(9Z)/25:1(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-0911000100-12b70874a203087696d2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-2911000100-abfb2a37f1f500dd9391JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-3912000000-682a48ba6d11cb8edebcJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-08gi-2973000110-5be417e70d695137b7d2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03e9-7794210020-4b60e800a89ebff6b9aaJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0bvi-5911000000-328c204b94e9d284fc95JSpectraViewer
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.