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CDP-DG(16:1(9Z)/18:1(11Z)) (YMDB12377)

Identification
YMDB IDYMDB12377
NameCDP-DG(16:1(9Z)/18:1(11Z))
SpeciesSaccharomyces cerevisiae
StrainBrewer's yeast
DescriptionCDP-DG(16:1(9Z)/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(16:1(9Z)/18:1(11Z)), in particular, consists of two 9Z-hexadecenoyl 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(16:1(9Z)/18:1(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: 978.108
Monoisotopic: 977.514292916
InChI KeyYOVNZDXBUXIJEK-HOXHGPEGSA-N
InChIInChI=1S/C46H81N3O15P2/c1-3-5-7-9-11-13-15-17-18-20-22-24-26-28-30-32-42(51)62-38(35-59-41(50)31-29-27-25-23-21-19-16-14-12-10-8-6-4-2)36-60-65(55,56)64-66(57,58)61-37-39-43(52)44(53)45(63-39)49-34-33-40(47)48-46(49)54/h13-16,33-34,38-39,43-45,52-53H,3-12,17-32,35-37H2,1-2H3,(H,55,56)(H,57,58)(H2,47,48,54)/b15-13-,16-14-/t38-,39-,43+,44?,45-/m1/s1
IUPAC Name{[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[(2R)-3-[(9Z)-hexadec-9-enoyloxy]-2-[(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)-3-[(9Z)-hexadec-9-enoyloxy]-2-[(11Z)-octadec-11-enoyloxy]propoxy(hydroxy)phosphoryl]oxy)phosphinic acid
Chemical FormulaC46H81N3O15P2
SMILES[H][C@@](COC(=O)CCCCCCC\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-5-phosphate
  • Pentose phosphate
  • N-glycosyl compound
  • Glycosyl compound
  • Pentose monosaccharide
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Pyrimidone
  • Fatty acid ester
  • Aminopyrimidine
  • Fatty acyl
  • Imidolactam
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Monosaccharide
  • Hydropyrimidine
  • Dicarboxylic acid or derivatives
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Carboxylic acid ester
  • Amino acid or derivatives
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Amine
  • Alcohol
  • 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 Solubility0.0046 g/LALOGPS
logP6.5ALOGPS
logP9.72ChemAxon
logS-5.3ALOGPS
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 Count42ChemAxon
Refractivity251.65 m³·mol⁻¹ChemAxon
Polarizability105.02 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(9Z)/16:1(9Z)/18:1(11Z))PW006678 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(12:0/16:0/16:1(9Z)/18:1(11Z))PW007196 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(12:0/16:1(11Z)/16:1(9Z)/18:1(11Z))PW007311 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(12:0/16:1(9Z)/16:1(9Z)/18:1(11Z))PW007426 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(14:0/14:0/16:1(9Z)/18:1(11Z))PW008193 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG PathwaysNot Available
SMPDB Reactions
PG(16:0/16:0) + CDP-DG(16:1(9Z)/18:1(11Z)) → Cytidine monophosphate + hydron + CL(12:0/14:1(9Z)/16:1(9Z)/18:1(11Z))
PG(16:0/16:0) + CDP-DG(16:1(9Z)/18:1(11Z)) → Cytidine monophosphate + hydron + CL(12:0/16:0/16:1(9Z)/18:1(11Z))
PG(16:0/16:0) + CDP-DG(16:1(9Z)/18:1(11Z)) → Cytidine monophosphate + hydron + CL(12:0/16:1(11Z)/16:1(9Z)/18:1(11Z))
PG(16:0/16:0) + CDP-DG(16:1(9Z)/18:1(11Z)) → Cytidine monophosphate + hydron + CL(12:0/16:1(9Z)/16:1(9Z)/18:1(11Z))
PG(14:0/14:0) + CDP-DG(16:1(9Z)/18:1(11Z)) → Cytidine monophosphate + hydron + CL(14:0/14:0/16:1(9Z)/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-0920000101-16abbc4a7733b6a74ad0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1920001000-f8ba7975fe86653ceec8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-3930000000-10dfc386ce6c158ea188JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0nni-0690001103-2808336df54f5a15d53cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0w30-5692200201-b78c5ab9829fab3fb575JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0bvi-5921000000-b5a8e83e13cdece3c8b5JSpectraViewer
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.