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CDP-DG(16:0/18:1(9Z)) (YMDB12318)

Identification
YMDB IDYMDB12318
NameCDP-DG(16:0/18:1(9Z))
SpeciesSaccharomyces cerevisiae
StrainBrewer's yeast
DescriptionCDP-DG(16:0/18:1(9Z)) 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(16:0/18:1(9Z)), 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(16:0/18:1(9Z)) is also a substrate of CDP-diacylglycerol pyrophosphatase. It is involved in CDP-diacylglycerol degradation pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 1-Hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-CDP
  • 1-Palmitoyl-2-oleoyl-sn-glycero-3-cytidine-5'-diphosphate
  • CDP-DG(16:0/18:1)
  • CDP-DG(16:0/18:1N9)
  • CDP-DG(16:0/18:1W9)
  • CDP-DG(34:1)
  • CDP-Diacylglycerol(16:0/18:1)
  • CDP-Diacylglycerol(16:0/18:1N9)
  • CDP-Diacylglycerol(16:0/18:1W9)
  • CDP-Diacylglycerol(34:1)
CAS numberNot Available
WeightAverage: 980.124
Monoisotopic: 979.529942981
InChI KeyFPQIENQTTUVFMM-BLPYJZGISA-N
InChIInChI=1S/C46H83N3O15P2/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/h17-18,33-34,38-39,43-45,52-53H,3-16,19-32,35-37H2,1-2H3,(H,55,56)(H,57,58)(H2,47,48,54)/b18-17-/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-(hexadecanoyloxy)-2-[(9Z)-octadec-9-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-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propoxy(hydroxy)phosphoryl]oxy)phosphinic acid
Chemical FormulaC46H83N3O15P2
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)CCCCCCC\C=C/CCCCCCCC
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 Solubility0.0043 g/LALOGPS
logP6.51ALOGPS
logP10.08ChemAxon
logS-5.4ALOGPS
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 Count43ChemAxon
Refractivity250.53 m³·mol⁻¹ChemAxon
Polarizability107.85 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(14:0/14:0/16:0/18:1(9Z))PW008158 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(14:0/14:1(11Z)/16:0/18:1(9Z))PW008340 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(14:0/14:1(9Z)/16:0/18:1(9Z))PW008541 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(14:0/16:0/16:0/18:1(9Z))PW008961 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(14:1(11Z)/14:1(11Z)/16:0/18:1(9Z))PW009392 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG PathwaysNot Available
SMPDB Reactions
PA(16:0/18:1(9Z)) + hydron + Cytidine triphosphate → Pyrophosphate + CDP-DG(16:0/18:1(9Z))
CDP-DG(16:0/18:1(9Z)) + Glycerol 3-phosphate → PGP(16:0/18:1(9Z)) + hydron + Cytidine monophosphate
PG(16:0/16:0) + CDP-DG(16:0/18:1(9Z)) → Cytidine monophosphate + hydron + CL(10:0/16:0/16:0/18:1(9Z))
PG(16:0/16:0) + CDP-DG(16:0/18:1(9Z)) → Cytidine monophosphate + hydron + CL(12:0/14:0/16:0/18:1(9Z))
PG(16:0/16:0) + CDP-DG(16:0/18:1(9Z)) → Cytidine monophosphate + hydron + CL(12:0/14:1(11Z)/16:0/18:1(9Z))
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-ea6baebdf45bc88e5c89JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1920001000-759c7de95464117a82fcJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-3930000000-2400c768c5541ff36a0dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0bt9-0690001103-4f74ac749916951ea91dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0bti-5692200201-8d93f2d99c9b78989b01JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-5921000000-647a4569c3e602e928caJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-2000010039-f248aeb627d3db6ee29bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-07w9-6000000096-a9f03535eca693b8334bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00di-0025910000-473ea5a7377e93fbc270JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0000001009-edcd69c729b370a00970JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004l-9071812302-4dbc8f5a66229b3c70faJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0c0r-6469401102-c12fd0a8cc5b1195d26bJSpectraViewer
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 IDHMDB0006971
Pubchem Compound ID53477915
Kegg IDNot Available
ChemSpider ID24765811
FOODB IDFDB024165
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