CDP-DG(18:1(9Z)/28:0) (YMDB12481)

Identification
YMDB IDYMDB12481
NameCDP-DG(18:1(9Z)/28:0)
SpeciesSaccharomyces cerevisiae
StrainBrewer's yeast
DescriptionCDP-DG(18:1(9Z)/28:0) 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)/28:0), 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)/28:0) 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: 1148.448
Monoisotopic: 1147.717743753
InChI KeyYDKQJFRRRZOYLD-CKALZMEZSA-N
InChIInChI=1S/C58H107N3O15P2/c1-3-5-7-9-11-13-15-17-19-20-21-22-23-24-25-26-27-28-30-32-34-36-38-40-42-44-54(63)74-50(47-71-53(62)43-41-39-37-35-33-31-29-18-16-14-12-10-8-6-4-2)48-72-77(67,68)76-78(69,70)73-49-51-55(64)56(65)57(75-51)61-46-45-52(59)60-58(61)66/h18,29,45-46,50-51,55-57,64-65H,3-17,19-28,30-44,47-49H2,1-2H3,(H,67,68)(H,69,70)(H2,59,60,66)/b29-18-/t50-,51-,55+,56?,57-/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-(octacosanoyloxy)-3-[(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)-2-(octacosanoyloxy)-3-[(9Z)-octadec-9-enoyloxy]propoxy)phosphoryl]oxy)phosphinic acid
Chemical FormulaC58H107N3O15P2
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)CCCCCCCCCCCCCCCCCCCCCCCCCCC
Chemical Taxonomy
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.00042 g/LALOGPS
logP8.44ALOGPS
logP15.42ChemAxon
logS-6.4ALOGPS
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 Count55ChemAxon
Refractivity305.74 m³·mol⁻¹ChemAxon
Polarizability133.2 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(10:0/10:0/18:1(9Z)/28:0)PW003617 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/12:0/18:1(9Z)/28:0)PW003892 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/14:0/18:1(9Z)/28:0)PW004182 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/14:1(11Z)/18:1(9Z)/28:0)PW004423 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/14:1(9Z)/18:1(9Z)/28:0)PW004664 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG PathwaysNot Available
SMPDB Reactions
PG(10:0/10:0) + CDP-DG(18:1(9Z)/28:0) → Cytidine monophosphate + hydron + CL(16:0/16:0/16:0/16:0)
PG(16:0/16:0) + CDP-DG(18:1(9Z)/28:0) → Cytidine monophosphate + hydron + CL(16:0/16:0/16:0/16:0)
PG(10:0/10:0) + CDP-DG(18:1(9Z)/28:0) → Cytidine monophosphate + hydron + CL(10:0/10:0/18:1(9Z)/28:0)
PG(16:0/16:0) + CDP-DG(18:1(9Z)/28:0) → Cytidine monophosphate + hydron + CL(10:0/12:0/18:1(9Z)/28:0)
PG(16:0/16:0) + CDP-DG(18:1(9Z)/28:0) → Cytidine monophosphate + hydron + CL(10:0/14:0/18:1(9Z)/28:0)
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-0910000100-174d3fe3a87995199b22JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1910000000-e827e7663c59d0e1fc66JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-3912000000-4c4a1b278085de26a33eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-08n9-0950200100-83d3278726085fdd7468JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03e9-6982301002-7908d152a4df1f81a140JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0bvi-5911000000-729456f028bb4b7c277dJSpectraViewer
MSMass Spectrum (Electron Ionization)Not 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 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.