CDP-DG(12:0(3-OH)/19:0cycv8c) (ECMDB24652) (M2MDB006769)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (2)
Record Information
Version2.0
Creation Date2015-09-08 19:53:55 -0600
Update Date2015-12-09 12:12:56 -0700
Secondary Accession Numbers
  • ECMDB24652
Identification
Name:CDP-DG(12:0(3-OH)/19:0cycv8c)
DescriptionCDP-DG(12:0(3-OH)/19:0cycv8c) 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 atoms. CDP-DG(12:0(3-OH)/19:0cycv8c), in particular, consists of one 3-hydroxydodecanoyl chain to C-1 atom, and one heptadec-11-12-cyclo-anoyl to the C-2 atom. 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(3-OH)/19:0cycv8c) is also a substrate of CDP-diacylglycerol pyrophosphatase. It is involved in CDP-diacylglycerol degradation pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:Not Available
Chemical Formula:C43H77N3O16P2
Weight:Average: 954.042
Monoisotopic: 953.477907407
InChI Key:LMCHDFLMJYYCAP-ZILQXWABSA-N
InChI:InChI=1S/C43H77N3O16P2/c1-3-5-7-9-11-15-19-23-34(47)28-39(49)57-29-35(60-38(48)24-20-16-13-10-12-14-18-22-33-27-32(33)21-17-8-6-4-2)30-58-63(53,54)62-64(55,56)59-31-36-40(50)41(51)42(61-36)46-26-25-37(44)45-43(46)52/h25-26,32-36,40-42,47,50-51H,3-24,27-31H2,1-2H3,(H,53,54)(H,55,56)(H2,44,45,52)/t32?,33?,34?,35-,36-,40+,41?,42-/m1/s1
CAS number:Not Available
IUPAC Name:{[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[(2R)-2-{[10-(2-hexylcyclopropyl)decanoyl]oxy}-3-[(3-hydroxydodecanoyl)oxy]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-{[10-(2-hexylcyclopropyl)decanoyl]oxy}-3-[(3-hydroxydodecanoyl)oxy]propoxy(hydroxy)phosphoryl]oxy)phosphinic acid
SMILES:[H][C@@](COC(=O)CC(O)CCCCCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCCC1CC1CCCCCC
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
  • Diacyl-glycerol-3-pyrophosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Beta-hydroxy acid
  • Fatty acid ester
  • Hydroxypyrimidine
  • Monoalkyl phosphate
  • Fatty acyl
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Dicarboxylic acid or derivatives
  • Hydropyrimidine
  • Hydroxy acid
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Heteroaromatic compound
  • Oxolane
  • Secondary alcohol
  • 1,2-diol
  • Carboxylic acid ester
  • Oxacycle
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Azacycle
  • Organooxygen compound
  • Organic oxide
  • Organic oxygen compound
  • Alcohol
  • Organic nitrogen compound
  • Carbonyl group
  • Organonitrogen compound
  • Hydrocarbon derivative
  • 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 Solubility0.02 g/LALOGPS
logP4.72ALOGPS
logP7.1ChemAxon
logS-4.7ALOGPS
pKa (Strongest Acidic)-0.032ChemAxon
pKa (Strongest Basic)3.27ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area283.5 ŲChemAxon
Rotatable Bond Count39ChemAxon
Refractivity235.22 m³·mol⁻¹ChemAxon
Polarizability103.38 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Membrane
Reactions:
2 DG(12:0(3-OH)/19:0cycv8c/0:0) + Cytidine triphosphate + Hydrogen ion >2 CDP-DG(12:0(3-OH)/19:0cycv8c) + Pyrophosphate
2 CDP-DG(12:0(3-OH)/19:0cycv8c) + Glycerol 3-phosphate >2 PGP(12:0(3-OH)/19:0cycv8c) + Cytidine monophosphate + Hydrogen ion + Cytidine monophosphate
SMPDB Pathways:
phospholipid biosynthesis (CL(12:0(3-OH)/19:0cycv8c/12:0(3-OH)/19:0cycv8c))PW001925 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-0910000001-08bdc716e63b0cb97057View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1910001000-bc08cad1312aaa7a27e8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-2920000000-4b9416d051b4b59e60eeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4j-0930001103-b0e3946175f464fde1ecView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-090s-4931100100-357158a1430f3cb64262View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0bvi-4921000000-fd8236c7869a01b7821eView in MoNA
MSMass Spectrum (Electron Ionization)Not AvailableView in JSpectraViewer
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
  • Uniprot Consortium (2012). "Reorganizing the protein space at the Universal Protein Resource (UniProt)." Nucleic Acids Res 40:D71-D75. Pubmed: 22102590
  • 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 IDNot Available
Kegg IDNot Available
ChemSpider 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:
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
2. 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.