CDP-1,2-didodecanoylglycerol (ECMDB21187) (M2MDB001596)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (4)XML
Proteins (4)
Record Information
Version2.0
Creation Date2012-07-30 14:54:48 -0600
Update Date2015-06-03 17:20:50 -0600
Secondary Accession Numbers
  • ECMDB21187
Identification
Name:CDP-1,2-didodecanoylglycerol
DescriptionCdp-1,2-didodecanoylglycerol belongs to the class of CDP-Diacylglycerols. These are glycerolipids containing a diacylglycerol, with a cytidine diphosphate attached to the oxygen O1 or O2 of the glycerol part. (inferred from compound structure)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
ValueSource
1,2-Didodecanoyl-sn-glycero-3-cytidine-5'-diphosphateChEBI
1,2-Dilauroyl-sn-glycero-3-cytidine 5'-diphosphateChEBI
CDP-1,2-Didodecanoyl-sn-glycerolChEBI
CDP-1,2-Dilauroyl-sn-glycerolChEBI
CDP-1,2-DilauroylglycerolChEBI
CDP-DG(12:0/12:0)ChEBI
1,2-Didodecanoyl-sn-glycero-3-cytidine-5'-diphosphoric acidGenerator
1,2-Dilauroyl-sn-glycero-3-cytidine 5'-diphosphoric acidGenerator
CDP-1,2-DidodecanoylglycerolChEBI
1,2-Didodecanoyl-sn-glycero-3-cytidine 5'-diphosphoric acidGenerator
Chemical Formula:C36H65N3O15P2
Weight:Average: 841.8599
Monoisotopic: 841.389091449
InChI Key:PTPPKXVNJJIECF-LSSKPTOFSA-N
InChI:InChI=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
CAS number:Not Available
IUPAC Name:[({[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy][(2R)-2,3-bis(dodecanoyloxy)propoxy]phosphinic acid
Traditional IUPAC Name:{[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(2R)-2,3-bis(dodecanoyloxy)propoxyphosphinic acid
SMILES:CCCCCCCCCCCC(=O)OC[C@H](COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](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
  • Fatty acid ester
  • Monoalkyl phosphate
  • Hydroxypyrimidine
  • Dicarboxylic acid or derivatives
  • Fatty acyl
  • Alkyl phosphate
  • Hydropyrimidine
  • Pyrimidine
  • Phosphoric acid ester
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Carboxylic acid ester
  • 1,2-diol
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Azacycle
  • Carboxylic acid derivative
  • Organopnictogen compound
  • Organic oxide
  • Alcohol
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.085 g/LALOGPS
logP3.78ALOGPS
logP5.73ChemAxon
logS-4ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)-0.52ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area263.27 ŲChemAxon
Rotatable Bond Count34ChemAxon
Refractivity203.4 m³·mol⁻¹ChemAxon
Polarizability86.93 ųChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Membrane
Reactions:
Cytidine triphosphate + Hydrogen ion + PA(16:0/16:0) > CDP-1,2-didodecanoylglycerol + Pyrophosphate
CDP-1,2-didodecanoylglycerol + Glycerol 3-phosphate > Cytidine monophosphate + Hydrogen ion + PGP(12:0/12:0)
CDP-1,2-didodecanoylglycerol + L-Serine > Cytidine monophosphate + Hydrogen ion + PS(16:0/16:0)
CDP-1,2-didodecanoylglycerol + Water > Cytidine monophosphate +2 Hydrogen ion + PA(16:0/16:0)
2 DG(12:0/12:0/0:0) + Cytidine triphosphate + Hydrogen ion >2 CDP-1,2-didodecanoylglycerol + Pyrophosphate
2 CDP-1,2-didodecanoylglycerol + Glycerol 3-phosphate >2 PGP(12:0/12:0) + Cytidine monophosphate + Hydrogen ion + Cytidine monophosphate
SMPDB Pathways:
phospholipid biosynthesis (CL(12:0(3-OH)/12:0(3-OH)/12:0/12:0))PW001915 ThumbThumb?image type=greyscaleThumb?image type=simple
phospholipid biosynthesis (CL(12:0/12:0/12:0/12:0))PW001930 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:Not Available
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900001010-903f4758ee3c8f4e97a3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1900000000-e13f2ee21e9108abb203View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-2920000000-fc72c3890c6df31f223dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0bu4-0900002110-7e32c57b209b0ce7bbbbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01ot-2901110000-af3d7258a954a21ffcdfView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0bvi-4900000000-23afda044a3033394634View in MoNA
MSMass Spectrum (Electron Ionization)Not AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Yurtsever D. (2007). Fatty acid methyl ester profiling of Enterococcus and Esherichia coli for microbial source tracking. M.sc. Thesis. Villanova University: U.S.A
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID34046
HMDB IDNot Available
Pubchem Compound ID118987286
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. CDP-diacylglycerol pyrophosphatase
General function:
Involved in CDP-diacylglycerol diphosphatase activity
Specific function:
CDP-diacylglycerol + H(2)O = CMP + phosphatidate
Gene Name:
cdh
Uniprot ID:
P06282
Molecular weight:
28451
Reactions
CDP-diacylglycerol + H(2)O = CMP + phosphatidate.
Protein Details
2. CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
General function:
Involved in phosphotransferase activity, for other substituted phosphate groups
Specific function:
This protein catalyzes the committed step to the synthesis of the acidic phospholipids
Gene Name:
pgsA
Uniprot ID:
P0ABF8
Molecular weight:
20700
Reactions
CDP-diacylglycerol + sn-glycerol 3-phosphate = CMP + 3(3-sn-phosphatidyl)-sn-glycerol 1-phosphate.
Protein Details
3. Phosphatidate cytidylyltransferase
General function:
Involved in transferase activity, transferring phosphorus-containing groups
Specific function:
CTP + phosphatidate = diphosphate + CDP- diacylglycerol
Gene Name:
cdsA
Uniprot ID:
P0ABG1
Molecular weight:
31453
Reactions
CTP + phosphatidate = diphosphate + CDP-diacylglycerol.
Protein Details
4. CDP-diacylglycerol--serine O-phosphatidyltransferase
General function:
Involved in phosphotransferase activity, for other substituted phosphate groups
Specific function:
CDP-diacylglycerol + L-serine = CMP + (3-sn- phosphatidyl)-L-serine
Gene Name:
pssA
Uniprot ID:
P23830
Molecular weight:
52801
Reactions
CDP-diacylglycerol + L-serine = CMP + (3-sn-phosphatidyl)-L-serine.