2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol (PAMDB000898)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000898
Identification
Name: 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
Description:2-phospho-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.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL 2-PHOSPHATE
  • 4-DIPHOSPHOCYTIDYL-2-C-methyl-D-erythritol 2-phosphoric acid
  • 4-Diphosphocytidyl-2-C-methylerythritol 2-phosphate
  • 4-Diphosphocytidyl-2-C-methylerythritol 2-phosphoric acid
  • 4-Diphosphocytidyl-2c Methylerythritol 2-phosphate
  • 4-Diphosphocytidyl-2C methylerythritol 2-phosphoric acid
  • 4-Diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate
  • 4-Diphosphocytidyl-2C-methyl-D-erythritol 2-phosphoric acid
  • CDP-ME-2P
  • CDP-Methyl-D-erylthritol 2-phosphate
  • CDP-Methyl-D-erylthritol 2-phosphoric acid
  • PPCytMeEryP
  • SUD
Chemical Formula: C14H22N3O17P3
Average Molecular Weight: 597.257
Monoisotopic Molecular Weight: 597.018401574
InChI Key: HTJXTKBIUVFUAR-XHIBXCGHSA-J
InChI:InChI=1S/C14H26N3O17P3/c1-14(6-18,33-35(23,24)25)8(19)5-31-37(28,29)34-36(26,27)30-4-7-10(20)11(21)12(32-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21H,4-6H2,1H3,(H,26,27)(H,28,29)(H2,15,16,22)(H2,23,24,25)/p-4/t7-,8-,10-,11-,12-,14+/m1/s1
CAS number: Not Available
IUPAC Name:{[(2S,3R)-4-({[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-1,3-dihydroxy-2-methylbutan-2-yl]oxy}phosphonic acid
Traditional IUPAC Name: [(2S,3R)-4-[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,3-dihydroxy-2-methylbutan-2-yl]oxyphosphonic acid
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)(CO)OP([O-])([O-])=O
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
  • Oxolane
  • Secondary alcohol
  • 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:-4
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility9.98 mg/mLALOGPS
logP-1.1ALOGPS
logP-5.5ChemAxon
logS-1.8ALOGPS
pKa (Strongest Acidic)1.05ChemAxon
pKa (Strongest Basic)1.85ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count16ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area318.88 Å2ChemAxon
Rotatable Bond Count13ChemAxon
Refractivity125.91 m3·mol-1ChemAxon
Polarizability48.74 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol <> 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + Cytidine monophosphate
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
2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol > 2-C-Methyl-D-erythritol 2,4-cyclodiphosphate + Cytidine monophosphate
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
2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol + 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol > Cytidine monophosphate + 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + Cytidine monophosphate
2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol + 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol > 2-C-Methyl-D-erythritol 2,4-cyclodiphosphate + Cytidine monophosphate + Cytidine monophosphate
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-1900010000-23a4ee9860d27e357bb0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1900000000-ac2d62a2bad3cc2b9d09View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-8910000000-9ba03b1df6c8e4cd78c6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0w29-4901043000-b5fbdc577444608870daView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-056r-9707010000-50a4154a2160feaa8e43View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-06vi-8901000000-f3de08e80f369b37214bView 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
  • 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
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID16840
HMDB IDNot Available
Pubchem Compound ID443200
Kegg IDC11436
ChemSpider ID391472
Wikipedia IDNot Available
BioCyc ID2-PHOSPHO-4-CYTIDINE-5-DIPHOSPHO-2-C-MET
EcoCyc ID2-PHOSPHO-4-CYTIDINE-5-DIPHOSPHO-2-C-MET
Ligand ExpoSUD