4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol (ECMDB20083) (M2MDB000931)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (785)
Record Information
Version2.0
Creation Date2012-05-31 14:26:32 -0600
Update Date2015-09-17 15:42:09 -0600
Secondary Accession Numbers
  • ECMDB20083
Identification
Name:4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol
Description4-(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
MOLSDFPDBSMILESInChI
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
Weight:Average: 519.294
Monoisotopic: 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
Description belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine ribonucleotides
Direct ParentPyrimidine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Pyrimidine ribonucleoside diphosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Pentose monosaccharide
  • Aminopyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Imidolactam
  • Alkyl phosphate
  • Tetrahydrofuran
  • Tertiary alcohol
  • Heteroaromatic compound
  • Secondary alcohol
  • Polyol
  • Azacycle
  • Oxacycle
  • Organoheterocyclic compound
  • Alcohol
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Amine
  • Organic oxide
  • Organooxygen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Primary alcohol
  • Primary amine
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility10.8 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count11ChemAxon
Refractivity115.04 m³·mol⁻¹ChemAxon
Polarizability44.23 ųChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol + Adenosine triphosphate <> 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol + ADP + Hydrogen ion
2-C-Methyl-D-erythritol-4-phosphate + Cytidine triphosphate + Hydrogen ion <> 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol + Pyrophosphate
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
Cytidine triphosphate + 2-C-methyl-D-erythritol 4-phosphate > Pyrophosphate + 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol
Adenosine triphosphate + 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol > ADP + 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
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
4 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol + Adenosine triphosphate <>2 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol + ADP + Hydrogen ion
4 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol + Adenosine triphosphate <>2 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol + ADP + Hydrogen ion
SMPDB Pathways:
Secondary metabolites: isoprenoid biosynthesis (nonmevalonate pathway)PW000975 ThumbThumb?image type=greyscaleThumb?image type=simple
Secondary metabolites: methylerythritol phosphate and polyisoprenoid biosynthesisPW000958 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, Positivesplash10-03di-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
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0f79-0002980000-b0c2dd0f91aa67816b82View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-08ou-0689210000-ce579339d5226e7cf795View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0gvp-4975000000-183cd21e1b0b0bbffbddView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-0000090000-641c25f0d0828a8b13d8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00fr-4211970000-3141df7963d44155286bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9134000000-c51a8f7c77198cc212bdView 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 IDHMDB0304166
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

Enzymes

Protein Details
1. 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
General function:
Involved in ATP binding
Specific function:
Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol. Phosphorylates isopentenyl phosphate at low rates. Also acts on isopentenol, and, much less efficiently, dimethylallyl alcohol. Dimethylallyl monophosphate does not serve as a substrate
Gene Name:
ispE
Uniprot ID:
P62615
Molecular weight:
30925
Reactions
ATP + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = ADP + 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol.
Protein Details
2. 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
General function:
Involved in catalytic activity
Specific function:
Catalyzes the formation of 4-diphosphocytidyl-2-C- methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4- phosphate (MEP)
Gene Name:
ispD
Uniprot ID:
Q46893
Molecular weight:
25737
Reactions
CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol.