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CDP-DG(18:1(11Z)/18:1(9Z)) (YMDB12433)

Identification
YMDB IDYMDB12433
NameCDP-DG(18:1(11Z)/18:1(9Z))
SpeciesSaccharomyces cerevisiae
StrainBrewer's yeast
DescriptionCDP-DG(18:1(11Z)/18:1(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(18:1(11Z)/18:1(9Z)), in particular, consists of two 11Z-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(11Z)/18:1(9Z)) is also a substrate of CDP-diacylglycerol pyrophosphatase. It is involved in CDP-diacylglycerol degradation pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 1-(11Z-Octadecenoyl)-2-(9Z-octadecenoyl)-sn-glycero-3-CDP
  • 1-Vaccenoyl-2-oleoyl-sn-glycero-3-cytidine-5'-diphosphate
  • CDP-DG(18:1/18:1)
  • CDP-DG(18:1N7/18:1N9)
  • CDP-DG(18:1W7/18:1W9)
  • CDP-DG(36:2)
  • CDP-Diacylglycerol(18:1/18:1)
  • CDP-Diacylglycerol(18:1N7/18:1N9)
  • CDP-Diacylglycerol(18:1W7/18:1W9)
  • CDP-Diacylglycerol(36:2)
CAS numberNot Available
WeightAverage: 1006.162
Monoisotopic: 1005.545593045
InChI KeyMJTZWNDRIHJESM-GZSUXWSDSA-N
InChIInChI=1S/C48H85N3O15P2/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-43(52)61-37-40(64-44(53)34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2)38-62-67(57,58)66-68(59,60)63-39-41-45(54)46(55)47(65-41)51-36-35-42(49)50-48(51)56/h13,15,18,20,35-36,40-41,45-47,54-55H,3-12,14,16-17,19,21-34,37-39H2,1-2H3,(H,57,58)(H,59,60)(H2,49,50,56)/b15-13-,20-18-/t40-,41-,45+,46?,47-/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-[(11Z)-octadec-11-enoyloxy]-2-[(9Z)-octadec-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-[(11Z)-octadec-11-enoyloxy]-2-[(9Z)-octadec-9-enoyloxy]propoxy)phosphoryl]oxy)phosphinic acid
Chemical FormulaC48H85N3O15P2
SMILES[H][C@@](COC(=O)CCCCCCCCC\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)CCCCCCC\C=C/CCCCCCCC
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
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.0029 g/LALOGPS
logP6.89ALOGPS
logP10.61ChemAxon
logS-5.5ALOGPS
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 Count44ChemAxon
Refractivity260.85 m³·mol⁻¹ChemAxon
Polarizability110.38 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(10:0/14:0/18:1(11Z)/18:1(9Z))PW004151 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/14:1(11Z)/18:1(11Z)/18:1(9Z))PW004392 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/14:1(9Z)/18:1(11Z)/18:1(9Z))PW004633 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/16:0/18:1(11Z)/18:1(9Z))PW005240 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/16:1(11Z)/18:1(11Z)/18:1(9Z))PW005384 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG PathwaysNot Available
SMPDB Reactions
PG(14:0/18:1(9Z)) + CDP-DG(18:1(11Z)/18:1(9Z)) → Cytidine monophosphate + hydron + CL(14:0/18:1(9Z)/18:1(11Z)/18:1(9Z))
PG(14:1(11Z)/16:1(11Z)) + CDP-DG(18:1(11Z)/18:1(9Z)) → Cytidine monophosphate + hydron + CL(14:1(11Z)/16:1(11Z)/18:1(11Z)/18:1(9Z))
PG(14:1(11Z)/16:1(9Z)) + CDP-DG(18:1(11Z)/18:1(9Z)) → Cytidine monophosphate + hydron + CL(14:1(11Z)/16:1(9Z)/18:1(11Z)/18:1(9Z))
PG(14:1(11Z)/18:0) + CDP-DG(18:1(11Z)/18:1(9Z)) → Cytidine monophosphate + hydron + CL(14:1(11Z)/18:0/18:1(11Z)/18:1(9Z))
PG(14:1(11Z)/18:1(11Z)) + CDP-DG(18:1(11Z)/18:1(9Z)) → Cytidine monophosphate + hydron + CL(14:1(11Z)/18:1(11Z)/18:1(11Z)/18:1(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, Negativesplash10-08gi-2980000402-0b833292e0622a8d5030JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03e9-5792300401-c45a13e1927da3703c28JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0bvi-4910000000-7449678af954180de28bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-9000000100-798f9fa3bfcd8f471729JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0036-8040900600-c8132aaed5599133b4adJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-053r-5439401501-0f854a2b027c0ae1e59dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0910000101-be986c807917ada54072JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1910001100-494878c07c599ebb4bacJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-3911000100-1c2fa2da9ae12299cd74JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-9101001047-a0e607276a06a6863d25JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4i-6000000069-05ee29f90dfc1585b9fbJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00di-0024900000-4526e83548c3b39ddd1fJSpectraViewer
MSMass Spectrum (Electron Ionization)Not AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot 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 IDHMDB0006989
Pubchem Compound ID53477932
Kegg IDNot Available
ChemSpider ID24765829
FOODB IDFDB024183
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.