CDP-1,2-Dioctadecanoylglycerol (ECMDB21191) (M2MDB001600)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (4)XML
Proteins (4)
Record Information
Version2.0
Creation Date2012-07-30 14:54:48 -0600
Update Date2015-06-03 17:20:51 -0600
Secondary Accession Numbers
  • ECMDB21191
Identification
Name:CDP-1,2-Dioctadecanoylglycerol
DescriptionCdp-1,2-dioctadecanoylglycerol 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:
  • CDP-1,2-dioctadecanoylglycerol
Chemical Formula:C48H87N3O15P2
Weight:Average: 1008.163
Monoisotopic: 1007.561242153
InChI Key:PDCWLWQTNQCGRI-IGIWICMZSA-L
InChI:InChI=1S/C48H89N3O15P2/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-43(52)61-37-40(64-44(53)34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2)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)/p-2/t40-,41-,45-,46-,47-/m1/s1
CAS number:Not Available
IUPAC Name:(2R)-2,3-bis(octadecanoyloxy)propyl ({[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphonato}oxy)phosphonate
Traditional IUPAC Name:(2R)-2,3-bis(octadecanoyloxy)propyl {[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphonato}oxyphosphonate
SMILES:[H]O[C@@]1([H])[C@@]([H])(O[C@]([H])(C([H])([H])OP([O-])(=O)OP([O-])(=O)OC([H])([H])[C@]([H])(OC(=O)C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H])C([H])([H])OC(=O)C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H])[C@@]1([H])O[H])N1C([H])=C([H])C(=NC1=O)N([H])[H]
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
  • 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
  • Organic anion
  • 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 Solubility0.0022 g/LALOGPS
logP6.94ALOGPS
logP11.06ChemAxon
logS-5.7ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)-0.52ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area268.93 ŲChemAxon
Rotatable Bond Count46ChemAxon
Refractivity256.37 m³·mol⁻¹ChemAxon
Polarizability113.97 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-Dioctadecanoylglycerol + Pyrophosphate
CDP-1,2-Dioctadecanoylglycerol + Glycerol 3-phosphate > Cytidine monophosphate + Hydrogen ion + PGP(18:0/18:0)
CDP-1,2-Dioctadecanoylglycerol + L-Serine > Cytidine monophosphate + Hydrogen ion + PS(16:0/16:0)
CDP-1,2-Dioctadecanoylglycerol + Water > Cytidine monophosphate +2 Hydrogen ion + PA(16:0/16:0)
Cytidine triphosphate + Hydrogen ion + PA(18:0/18:0) > Pyrophosphate + CDP-1,2-Dioctadecanoylglycerol
L-Serine + CDP-1,2-Dioctadecanoylglycerol + L-Serine > Hydrogen ion + Cytidine monophosphate + PS(18:0/18:0) + Cytidine monophosphate
Glycerol 3-phosphate + CDP-1,2-Dioctadecanoylglycerol > Hydrogen ion + Cytidine monophosphate + PGP(18:0/18:0) + Cytidine monophosphate
SMPDB Pathways:
phospholipid biosynthesis I (18:0, 18:0)PW001001 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-9030000000-e1a064a9abea7e6c72c1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4r-9270000002-acbd6c380a809f73c4f4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-07g0-4982000000-4753db19d8f2995f1435View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a59-9050000001-77fe6ca4756044deb06fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0pc0-9370000000-444456fa8f11cc184314View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-001i-7390000000-fb009b9fa023ac5f170dView in MoNA
References
References:
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • 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 IDNot Available
HMDB IDNot Available
Pubchem Compound ID49859559
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.