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CDP-DG(12:0/12:0) (YMDB12100)

Identification
YMDB IDYMDB12100
NameCDP-DG(12:0/12:0)
SpeciesSaccharomyces cerevisiae
StrainBrewer's yeast
DescriptionCDP-DG(12:0/12:0) 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(12:0/12:0), in particular, consists of two dodecanoyl 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(12:0/12:0) 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: 841.87
Monoisotopic: 841.389092401
InChI KeyPTPPKXVNJJIECF-MYNNLVAUSA-N
InChIInChI=1S/C36H65N3O15P2/c1-3-5-7-9-11-13-15-17-19-21-31(40)49-25-28(52-32(41)22-20-18-16-14-12-10-8-6-4-2)26-50-55(45,46)54-56(47,48)51-27-29-33(42)34(43)35(53-29)39-24-23-30(37)38-36(39)44/h23-24,28-29,33-35,42-43H,3-22,25-27H2,1-2H3,(H,45,46)(H,47,48)(H2,37,38,44)/t28-,29-,33+,34?,35-/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(dodecanoyloxy)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(dodecanoyloxy)propoxy(hydroxy)phosphoryl]oxy)phosphinic acid
Chemical FormulaC36H65N3O15P2
SMILES[H][C@@](COC(=O)CCCCCCCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCCCC
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 Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.085 g/LALOGPS
logP3.78ALOGPS
logP6ChemAxon
logS-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 Count34ChemAxon
Refractivity203.4 m³·mol⁻¹ChemAxon
Polarizability88.79 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(12:0/12:0/12:0/22:0)PW005875 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(12:0/12:0/12:0/24:0)PW005876 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(12:0/12:0/12:0/24:1(11Z))PW005877 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(12:0/12:0/12:0/24:1(9Z))PW005878 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(12:0/12:0/12:0/26:0)PW005879 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG PathwaysNot Available
SMPDB Reactions
PA(12:0/12:0) + hydron + Cytidine triphosphate → Pyrophosphate + CDP-DG(12:0/12:0)
CDP-DG(12:0/12:0) + Glycerol 3-phosphate → PGP(12:0/12:0) + hydron + Cytidine monophosphate
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-0900001010-a682f4961688270d84e7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1900000000-c8495e961459f8b4cf16JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-3920000000-cc03a5c34ebc18d571f8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a5d-0900001110-c75d27859abe566d084bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01pk-3901111000-497977aaeffa3ed56979JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0bvi-4900000000-ddcf16f2c827eb37e2d0JSpectraViewer
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 ID3247021
Kegg IDNot Available
ChemSpider IDNot Available
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
General function:
Involved in phosphotransferase activity, for other substituted phosphate groups
Specific function:
Essential for the viability of mitochondrial petite mutant. Catalyzes the committed step to the synthesis of the acidic phospholipids
Gene Name:
PGS1
Uniprot ID:
P25578
Molecular weight:
59369.69922
Reactions
CDP-diacylglycerol + sn-glycerol 3-phosphate → CMP + 3(3-sn-phosphatidyl)-sn-glycerol 1-phosphate.
Protein Details
2. Phosphatidate cytidylyltransferase
General function:
Involved in transferase activity, transferring phosphorus-containing groups
Specific function:
Supplies CDP-diacylglycerol, which may play an important role as both a precursor to phosphoinositide biosynthesis in the plasma membrane and as a negative effector of phosphatidylinositol 4-kinase activity, thereby exerting an effect on cell proliferation via a lipid-dependent signal transduction cascade
Gene Name:
CDS1
Uniprot ID:
P38221
Molecular weight:
51822.39844
Reactions
CTP + phosphatidate → diphosphate + CDP-diacylglycerol.
Protein Details
3. Phosphatidate cytidylyltransferase, mitochondrial
General function:
CDP-diacylglycerol biosynthetic process
Specific function:
Catalyzes the formation of CDP-diacylglycerol (CDP-DAG) from phosphatidic acid (PA) in the mitochondrial inner membrane. Required for the biosynthesis of the dimeric phospholipid cardiolipin, which stabilizes supercomplexes of the mitochondrial respiratory chain in the mitochondrial inner membrane.
Gene Name:
TAM41
Uniprot ID:
P53230
Molecular weight:
44199.33
Reactions