CDP-DG(10:0/12:0) (ECMDB23323) (M2MDB003713)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (3)Transporters (3)XML
Proteins (6)
Record Information
Version2.0
Creation Date2012-10-11 06:39:33 -0600
Update Date2015-12-09 12:12:38 -0700
Secondary Accession Numbers
  • ECMDB23323
Identification
Name:CDP-DG(10:0/12:0)
DescriptionCDP-DG(10:0/12:0) 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 atoms. CDP-DG(10:0/12:0), in particular, consists of one decanoyl chain to C-1 atom, and one dodecanoyl 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(10:0/12:0) is also a substrate of CDP-diacylglycerol pyrophosphatase. It is involved in CDP-diacylglycerol degradation pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 1-decanoyl-2-dodecanoyl-sn-glycero-3-CDP
  • 1-decanoyl-2-dodecanoyl-sn-glycero-3-cytidine-5'-diphosphate
  • 1-decanoyl-2-dodecanoyl-sn-glycero-3-cytidine-5'-diphosphate
  • 1-Decanoyl-2-dodecanoyl-sn-glycero-3-cytidine-5'-diphosphoric acid
  • CDP-DG(22:0)
  • CDP-Diacylglycerol(10:0/12:0)
  • CDP-Diacylglycerol(22:0)
Chemical Formula:C34H61N3O15P2
Weight:Average: 813.816
Monoisotopic: 813.357792272
InChI Key:VCAJBPAUQYCALG-MJRBPZOSSA-N
InChI:InChI=1S/C34H61N3O15P2/c1-3-5-7-9-11-12-14-16-18-20-30(39)50-26(23-47-29(38)19-17-15-13-10-8-6-4-2)24-48-53(43,44)52-54(45,46)49-25-27-31(40)32(41)33(51-27)37-22-21-28(35)36-34(37)42/h21-22,26-27,31-33,40-41H,3-20,23-25H2,1-2H3,(H,43,44)(H,45,46)(H2,35,36,42)/t26-,27-,31+,32?,33-/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)-3-(decanoyloxy)-2-(dodecanoyloxy)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-(decanoyloxy)-2-(dodecanoyloxy)propoxy(hydroxy)phosphoryl]oxy)phosphinic acid
SMILES:[H][C@@](COC(=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)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-5-phosphate
  • Pentose phosphate
  • N-glycosyl compound
  • Glycosyl compound
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Hydroxypyrimidine
  • Monoalkyl phosphate
  • Fatty acid ester
  • Fatty acyl
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Monosaccharide
  • Hydropyrimidine
  • Dicarboxylic acid or derivatives
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Carboxylic acid ester
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.21 g/LALOGPS
logP3.24ALOGPS
logP5.11ChemAxon
logS-3.6ALOGPS
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 Count32ChemAxon
Refractivity194.2 m³·mol⁻¹ChemAxon
Polarizability84.54 ųChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Membrane
Reactions:
Hydrogen ion + Cytidine triphosphate + CDP-DG(10:0/12:0) > Pyrophosphate + DG(10:0/12:0/0:0)
DG(10:0/12:0/0:0) + Hydrogen ion + Cytidine triphosphate > CDP-DG(10:0/12:0) + Pyrophosphate
CDP-DG(10:0/12:0) + L-Serine + L-Serine > PS(10:0(3-OH)/12:0(3-OH)) + Cytidine monophosphate + Hydrogen ion + Cytidine monophosphate
CDP-DG(10:0/12:0) + L-Serine + L-Serine > PS(10:0(3-OH)/12:0) + Cytidine monophosphate + Hydrogen ion + Cytidine monophosphate
CDP-DG(10:0/12:0) + L-Serine + L-Serine > PS(10:0/12:0(3-OH)) + Cytidine monophosphate + Hydrogen ion + Cytidine monophosphate
SMPDB Pathways:
phospholipid biosynthesis CDP-DG(10:0/12:0)PW001746 ThumbThumb?image type=greyscaleThumb?image type=simple
phospholipid biosynthesis CDP-DG(10:0/12:0) IIPW001818 ThumbThumb?image type=greyscaleThumb?image type=simple
phospholipid biosynthesis CDP-DG(10:0/12:0) IIIPW001819 ThumbThumb?image type=greyscaleThumb?image type=simple
phospholipid biosynthesis CDP-DG(10:0/12:0) IVPW001820 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900001000-c20faf0b09ff6b8baddaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1900000000-1c81188e1320ac0aa2adView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-2910000000-04dfc8b33bcd99fad7d2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0nt9-0900001100-0e8f6e2e30d6422216fcView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0jb9-2901110000-d3d1efb0187a6cdd1123View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0bvi-3900000000-0eb59f67b1bb631befe6View 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 IDNot Available
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. 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
2. Protein crcA
General function:
Not Available
Specific function:
Not known; overproduction leads to camphor resistance and chromosome condensation
Gene Name:
crcA
Uniprot ID:
P37001
Molecular weight:
21770
Protein Details
3. 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.

Transporters

Protein Details
1. Probable phospholipid ABC transporter-binding protein mlaB
General function:
Involved in phospholipid transporter activity
Specific function:
Part of the ABC transporter complex mlaFEDB that actively prevents phospholipid accumulation at the cell surface. Probably maintains lipid asymmetry in the outer membrane by retrograde trafficking of phospholipids from the outer membrane to the inner membrane
Gene Name:
mlaB
Uniprot ID:
P64602
Molecular weight:
10680
Protein Details
2. Probable phospholipid ABC transporter-binding protein mlaD
General function:
Secondary metabolites biosynthesis, transport and catabolism
Specific function:
Part of the ABC transporter complex mlaFEDB that actively prevents phospholipid accumulation at the cell surface. Probably maintains lipid asymmetry in the outer membrane by retrograde trafficking of phospholipids from the outer membrane to the inner membrane
Gene Name:
mlaD
Uniprot ID:
P64604
Molecular weight:
19576
Protein Details
3. Probable phospholipid ABC transporter permease protein mlaE
General function:
Secondary metabolites biosynthesis, transport and catabolism
Specific function:
Part of the ABC transporter complex mlaFEDB that actively prevents phospholipid accumulation at the cell surface. Probably maintains lipid asymmetry in the outer membrane by retrograde trafficking of phospholipids from the outer membrane to the inner membrane
Gene Name:
mlaE
Uniprot ID:
P64606
Molecular weight:
27863