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CDP-DG(16:0/20:0) (YMDB12319)

Identification
YMDB IDYMDB12319
NameCDP-DG(16:0/20:0)
SpeciesSaccharomyces cerevisiae
StrainBrewer's yeast
DescriptionCDP-DG(16:0/20:0) 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(16:0/20:0), in particular, consists of two hexadecanoyl 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(16:0/20:0) 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: 1010.194
Monoisotopic: 1009.576893174
InChI KeyVDLBHRCSCDSSER-KTSAPKHVSA-N
InChIInChI=1S/C48H89N3O15P2/c1-3-5-7-9-11-13-15-17-18-19-20-22-24-26-28-30-32-34-44(53)64-40(37-61-43(52)33-31-29-27-25-23-21-16-14-12-10-8-6-4-2)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/h35-36,40-41,45-47,54-55H,3-34,37-39H2,1-2H3,(H,57,58)(H,59,60)(H2,49,50,56)/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)-3-(hexadecanoyloxy)-2-(icosanoyloxy)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-(hexadecanoyloxy)-2-(icosanoyloxy)propoxy(hydroxy)phosphoryl]oxy)phosphinic acid
Chemical FormulaC48H89N3O15P2
SMILES[H][C@@](COC(=O)CCCCCCCCCCCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCCCCCCCCCCCC
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 Solubility0.0026 g/LALOGPS
logP6.87ALOGPS
logP11.34ChemAxon
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 Count46ChemAxon
Refractivity258.61 m³·mol⁻¹ChemAxon
Polarizability113.16 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(10:0/12:0/16:0/20:0)PW003807 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/14:0/16:0/20:0)PW004083 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/14:1(11Z)/16:0/20:0)PW004324 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/14:1(9Z)/16:0/20:0)PW004565 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/16:0/16:0/20:0)PW005167 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG PathwaysNot Available
SMPDB Reactions
PA(16:0/16:0) + hydron + Cytidine triphosphate → Pyrophosphate + CDP-DG(16:0/20:0)
CDP-DG(16:0/20:0) + Glycerol 3-phosphate → PGP(16:0/20:0) + hydron + Cytidine monophosphate
PG(16:0/16:0) + CDP-DG(16:0/20:0) → Cytidine monophosphate + hydron + CL(16:0/16:0/16:0/16:0)
PG(16:0/16:0) + CDP-DG(16:0/20:0) → Cytidine monophosphate + hydron + CL(10:0/12:0/16:0/20:0)
PG(16:0/16:0) + CDP-DG(16:0/20:0) → Cytidine monophosphate + hydron + CL(10:0/14:0/16:0/20:0)
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-0920001100-e9ae18ee476eb94f20afJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1920001000-6013938bf2e15d60e73eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-3930000000-742bc508d2d46dc8b3dcJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0bt9-1892001202-fffeef5ce1d382081262JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0bt9-5692110201-a5634c7761504eb000ffJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0bt9-5911000000-c86f5dd8e0a19faa0eb3JSpectraViewer
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. 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. 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.
Protein Details
4. 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