CDP-DG(18:0/18:1(11Z)) (YMDB12405)

Identification
YMDB IDYMDB12405
NameCDP-DG(18:0/18:1(11Z))
SpeciesSaccharomyces cerevisiae
StrainBrewer's yeast
DescriptionCDP-DG(18:0/18:1(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(18:0/18:1(11Z)), in particular, consists of two octadecanoyl 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(18:0/18:1(11Z)) is also a substrate of CDP-diacylglycerol pyrophosphatase. It is involved in CDP-diacylglycerol degradation pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 1-Octadecanoyl-2-(11Z-octadecenoyl)-sn-glycero-3-CDP
  • 1-Stearoyl-2-vaccenoyl-sn-glycero-3-cytidine-5'-diphosphate
  • CDP-DG(18:0/18:1)
  • CDP-DG(18:0/18:1N7)
  • CDP-DG(18:0/18:1W7)
  • CDP-DG(36:1)
  • CDP-Diacylglycerol(18:0/18:1)
  • CDP-Diacylglycerol(18:0/18:1N7)
  • CDP-Diacylglycerol(18:0/18:1W7)
  • CDP-Diacylglycerol(36:1)
CAS numberNot Available
WeightAverage: 1008.178
Monoisotopic: 1007.561243109
InChI KeyFBSLHTWQFOZAGL-DNLPIHBOSA-N
InChIInChI=1S/C48H87N3O15P2/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/h14,16,35-36,40-41,45-47,54-55H,3-13,15,17-34,37-39H2,1-2H3,(H,57,58)(H,59,60)(H2,49,50,56)/b16-14-/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}({hydroxy[(2R)-2-[(11Z)-octadec-11-enoyloxy]-3-(octadecanoyloxy)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)-2-[(11Z)-octadec-11-enoyloxy]-3-(octadecanoyloxy)propoxy)phosphoryl]oxy)phosphinic acid
Chemical FormulaC48H87N3O15P2
SMILES[H][C@@](COC(=O)CCCCCCCCCCCCCCCCC)(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 Solubility0.0027 g/LALOGPS
logP6.9ALOGPS
logP10.97ChemAxon
logS-5.6ALOGPS
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 Count45ChemAxon
Refractivity259.73 m³·mol⁻¹ChemAxon
Polarizability111.69 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(10:0/14:0/18:0/18:1(11Z))PW004132 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/14:1(11Z)/18:0/18:1(11Z))PW004373 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/14:1(9Z)/18:0/18:1(11Z))PW004614 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/16:0/18:0/18:1(11Z))PW005222 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/16:1(11Z)/18:0/18:1(11Z))PW005366 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG PathwaysNot Available
SMPDB Reactions
PG(16:0/16:0) + CDP-DG(18:0/18:1(11Z)) → Cytidine monophosphate + hydron + CL(10:0/14:0/18:0/18:1(11Z))
PG(16:0/16:0) + CDP-DG(18:0/18:1(11Z)) → Cytidine monophosphate + hydron + CL(10:0/14:1(11Z)/18:0/18:1(11Z))
PG(16:0/16:0) + CDP-DG(18:0/18:1(11Z)) → Cytidine monophosphate + hydron + CL(10:0/14:1(9Z)/18:0/18:1(11Z))
PG(16:0/16:0) + CDP-DG(18:0/18:1(11Z)) → Cytidine monophosphate + hydron + CL(10:0/16:0/18:0/18:1(11Z))
PG(16:0/16:0) + CDP-DG(18:0/18:1(11Z)) → Cytidine monophosphate + hydron + CL(10:0/16:1(11Z)/18:0/18:1(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-0910000200-91a9f7f8f6c6a1bdc833JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1910000100-c26874d2f64201c9bbccJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-3921000100-c928c66c8966d665ad33JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0ce9-2890000402-b28eab7ef450925d4434JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03yi-5692300301-25d0a96c3d9614f75035JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0bvi-5921000000-ee298c116ed20d149a48JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-9100001027-a8fcebb09bf04bf30363JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0apl-8100000089-7c88107083ee317c21a2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00di-0013900000-07db0cfc9afc9e806c3eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-9000000201-d9bee24ed92de09b64b4JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00o3-9060801400-aab63b2de74399035f58JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-05pk-9358501401-80293dfc50f904bc86adJSpectraViewer
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 IDHMDB0006979
Pubchem Compound ID53477923
Kegg IDNot Available
ChemSpider ID24765819
FOODB IDFDB024173
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.