4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol (PAMDB000931)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000931
Identification
Name: 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol
Description:4-(cytidine 5'-diphospho)-2-c-methyl-D-erythritol is a member of the chemical class known as Pyrimidine Ribonucleoside Diphosphates. These are pyrimidine ribobucleotides with diphosphate group linked to the ribose moiety. CDP-ME is an intermediate in the mevalonate-independent pathway for isoprenoid biosynthesis in a number of prokaryotic organisms, algae, the plant plastids and the malaria parasite. (PMID 11427897) In the MEP pathway, 4-diphosphocytidyl-2-C-methyl-D-erythritol is formed from 2-C-methyl-D-erythritol 4-phosphate (MEP) and CTP in a reaction catalyzed by a 4-diphosphocytidyl-2-C-methyl-D-erythritol synthase (IspD). (PMID 17921290) Diphosphocytidyl-methylerythritol (DPCME) synthetase is involved in the mevalonate-independent pathway of isoprenoid biosynthesis, where it catalyses the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from 2-C-methyl-D-erythritol 4-phosphate and CTP. (PMID 11468415)
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 4-CDP-2-C-Methyl-D-erythritol
  • 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL
  • 4-Diphosphocytidyl-2-C-methylerythritol
  • 4-Diphosphocytidyl-2C-methyl-D-erythritol
  • CDM
  • CDP-ME
  • CDP-Methyl-D-erythritol
  • PPCytMeEry
Chemical Formula: C14H23N3O14P2
Average Molecular Weight: 519.294
Monoisotopic Molecular Weight: 519.066623588
InChI Key: YFAUKWZNPVBCFF-XHIBXCGHSA-L
InChI:InChI=1S/C14H25N3O14P2/c1-14(23,6-18)8(19)5-29-33(26,27)31-32(24,25)28-4-7-10(20)11(21)12(30-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21,23H,4-6H2,1H3,(H,24,25)(H,26,27)(H2,15,16,22)/p-2/t7-,8-,10-,11-,12-,14+/m1/s1
CAS number: Not Available
IUPAC Name:[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy][(2R,3S)-2,3,4-trihydroxy-3-methylbutoxy]phosphinic acid
Traditional IUPAC Name: 4-cdp-2-C-methyl-D-erythritol
SMILES:[H][C@@](O)(COP(O)(=O)OP([O-])(=O)OC[C@@]1([H])O[C@@]([H])(N2C=CC(=N)N=C2[O-])[C@]([H])(O)[C@]1([H])O)[C@@](C)(O)CO
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribobucleotides with diphosphate group linked to the ribose moiety.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Pyrimidine nucleotides
Sub ClassPyrimidine ribonucleotides
Direct Parent Pyrimidine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Pyrimidine ribonucleoside diphosphate
  • N-glycosyl compound
  • Glycosyl compound
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Hydroxypyrimidine
  • Monoalkyl phosphate
  • Aminopyrimidine
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Monosaccharide
  • Hydropyrimidine
  • Saccharide
  • Heteroaromatic compound
  • Tertiary alcohol
  • Oxolane
  • Secondary alcohol
  • Polyol
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Not Available
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility10.8 mg/mLALOGPS
logP-1.8ALOGPS
logP-5.3ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
pKa (Strongest Basic)3.34ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area272.35 Å2ChemAxon
Rotatable Bond Count11ChemAxon
Refractivity115.04 m3·mol-1ChemAxon
Polarizability44.23 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
2-C-Methyl-D-erythritol-4-phosphate + Cytidine triphosphate <> 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol + Pyrophosphate
4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol + Adenosine triphosphate <> 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol + ADP
4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol + Adenosine triphosphate > Hydrogen ion + 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol + ADP
Hydrogen ion + 2-C-Methyl-D-erythritol-4-phosphate + Cytidine triphosphate > 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol + Pyrophosphate
2-C-methyl-D-erythritol 4-phosphate + Cytidine triphosphate + Hydrogen ion > Pyrophosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol + 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol
4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol + Adenosine triphosphate + 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol > Adenosine diphosphate + Hydrogen ion + 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol + ADP + 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900010000-dd055cf6bd442a418647View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-2900000000-4e622642413e6ebd8477View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-6900000000-74e9c9a2a9edbdec480fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-024i-8921880000-a4764a7c92b71559f802View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01t9-9873300000-13a6ee53acf7e6b82639View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0bvl-5900000000-5fb1217b0273b9eb07edView in MoNA
References
References:
  • Eoh, H., Brown, A. C., Buetow, L., Hunter, W. N., Parish, T., Kaur, D., Brennan, P. J., Crick, D. C. (2007). "Characterization of the Mycobacterium tuberculosis 4-diphosphocytidyl-2-C-methyl-D-erythritol synthase: potential for drug development." J Bacteriol 189:8922-8927. Pubmed: 17921290
  • 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
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID16578
HMDB IDNot Available
Pubchem Compound ID443199
Kegg IDC11435
ChemSpider ID391471
Wikipedia IDNot Available
BioCyc ID4-CYTIDINE-5-DIPHOSPHO-2-C
EcoCyc ID4-CYTIDINE-5-DIPHOSPHO-2-C
Ligand ExpoCDM