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CDP-DG(18:1(11Z)/18:1(11Z)) (YMDB12432)

Identification
YMDB IDYMDB12432
NameCDP-DG(18:1(11Z)/18:1(11Z))
SpeciesSaccharomyces cerevisiae
StrainBrewer's yeast
DescriptionCDP-DG(18:1(11Z)/18:1(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(11Z)/18:1(11Z)), 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(11Z)) is also a substrate of CDP-diacylglycerol pyrophosphatase. It is involved in CDP-diacylglycerol degradation pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 1,2-Di(11Z-octadecenoyl)-rac-glycero-3-CDP
  • 1,2-Divaccenoyl-rac-glycero-3-cytidine-5'-diphosphate
  • CDP-DG(18:1/18:1)
  • CDP-DG(18:1N7/18:1N7)
  • CDP-DG(18:1W7/18:1W7)
  • CDP-DG(36:2)
  • CDP-Diacylglycerol(18:1/18:1)
  • CDP-Diacylglycerol(18:1N7/18:1N7)
  • CDP-Diacylglycerol(18:1W7/18:1W7)
  • CDP-Diacylglycerol(36:2)
CAS numberNot Available
WeightAverage: 1006.162
Monoisotopic: 1005.545593045
InChI KeyKISJWPWNABZPGN-PYYNXHAWSA-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/h13-16,35-36,40-41,45-47,54-55H,3-12,17-34,37-39H2,1-2H3,(H,57,58)(H,59,60)(H2,49,50,56)/b15-13-,16-14-/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}({[(2R)-2,3-bis[(11Z)-octadec-11-enoyloxy]propoxy](hydroxy)phosphoryl}oxy)phosphinic acid
Traditional IUPAC Name[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([(2R)-2,3-bis[(11Z)-octadec-11-enoyloxy]propoxy(hydroxy)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)CCCCCCCCC\C=C/CCCCCC
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
logP6.88ALOGPS
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
Polarizability109.59 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(12:0/14:1(11Z)/18:1(11Z)/18:1(11Z))PW006492 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(12:0/14:1(9Z)/18:1(11Z)/18:1(11Z))PW006714 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(12:0/16:0/18:1(11Z)/18:1(11Z))PW007228 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(12:0/16:1(11Z)/18:1(11Z)/18:1(11Z))PW007343 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(12:0/16:1(9Z)/18:1(11Z)/18:1(11Z))PW007458 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG PathwaysNot Available
SMPDB Reactions
PG(16:0/16:0) + CDP-DG(18:1(11Z)/18:1(11Z)) → Cytidine monophosphate + hydron + CL(10:0/14:0/18:1(11Z)/18:1(11Z))
PG(16:0/16:0) + CDP-DG(18:1(11Z)/18:1(11Z)) → Cytidine monophosphate + hydron + CL(10:0/14:1(11Z)/18:1(11Z)/18:1(11Z))
PG(16:0/16:0) + CDP-DG(18:1(11Z)/18:1(11Z)) → Cytidine monophosphate + hydron + CL(10:0/14:1(9Z)/18:1(11Z)/18:1(11Z))
PG(16:0/16:0) + CDP-DG(18:1(11Z)/18:1(11Z)) → Cytidine monophosphate + hydron + CL(10:0/16:0/18:1(11Z)/18:1(11Z))
PG(16:0/16:0) + CDP-DG(18:1(11Z)/18:1(11Z)) → Cytidine monophosphate + hydron + CL(10:0/16:1(11Z)/18:1(11Z)/18:1(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-0910000101-b8e9b9b9fe55d9d9f062JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1910001100-7ddabefc3a67e3a347afJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-3911000100-547a27aca6d35b48d3f4JSpectraViewer
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, Positivesplash10-0a4i-9001001048-9e69e0f98776d938a662JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4i-5000000069-86123df0d8ad43e7aa9eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00di-0024900000-66a81ba5967cf70e7177JSpectraViewer
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 IDHMDB0006988
Pubchem Compound ID24779568
Kegg IDNot Available
ChemSpider ID24765828
FOODB IDFDB024182
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.