2-C-Methyl-D-erythritol-2,4-cyclodiphosphate (PAMDB000611)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000611
Identification
Name: 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate
Description:2-c-methyl-D-erythritol-2,4-cyclodiphosphate is a member of the chemical class known as Organic Pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 2-C-Methyl-D-erythritol-2,4-cyclodiphosphoric acid
  • ME-2,4cPP
  • MeEry2,4CP
Chemical Formula: C5H10O9P2
Average Molecular Weight: 276.075
Monoisotopic Molecular Weight: 275.980004942
InChI Key: SFRQRNJMIIUYDI-UHNVWZDZSA-L
InChI:InChI=1S/C5H12O9P2/c1-5(3-6)4(7)2-12-15(8,9)14-16(10,11)13-5/h4,6-7H,2-3H2,1H3,(H,8,9)(H,10,11)/p-2/t4-,5+/m1/s1
CAS number: 143488-44-2
IUPAC Name:(6S,7R)-7-hydroxy-6-(hydroxymethyl)-6-methyl-2,4-dioxo-1,3,5,2???4???trioxadiphosphocane-2,4-bis(olate)
Traditional IUPAC Name: (6S,7R)-7-hydroxy-6-(hydroxymethyl)-6-methyl-2,4-dioxo-1,3,5,2???4???trioxadiphosphocane-2,4-bis(olate)
SMILES:[H][C@@]1(O)COP([O-])(=O)OP([O-])(=O)O[C@@]1(C)CO
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.
Kingdom Organic compounds
Super ClassOrganooxygen compounds
Class Organic oxoanionic compounds
Sub ClassOrganic pyrophosphates
Direct Parent Organic pyrophosphates
Alternative Parents
Substituents
  • Organic pyrophosphate
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Organic anion
  • Aliphatic heteromonocyclic compound
Molecular Framework Aliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Not Available
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility54.6 mg/mLALOGPS
logP-1ALOGPS
logP-1.8ChemAxon
logS-0.76ALOGPS
pKa (Strongest Acidic)1.83ChemAxon
pKa (Strongest Basic)-3.1ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area148.41 Å2ChemAxon
Rotatable Bond Count1ChemAxon
Refractivity46.84 m3·mol-1ChemAxon
Polarizability19.85 Å3ChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + 2 Flavodoxin reduced + Hydrogen ion >2 flavodoxin semi oxidized + 1-Hydroxy-2-methyl-2-butenyl 4-diphosphate + Water
2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol <> 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + Cytidine monophosphate
2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + 2 Reduced ferredoxin + Oxidized ferredoxin <> 1-Hydroxy-2-methyl-2-butenyl 4-diphosphate + Water +2 Oxidized ferredoxin + Reduced ferredoxin
1-Hydroxy-2-methyl-2-butenyl 4-diphosphate + Water + Oxidized-ferredoxins < 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + Hydrogen ion + Reduced-ferredoxins
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-C-Methyl-D-erythritol-2,4-cyclodiphosphate + a reduced flavodoxin > Water + Hydrogen ion + an oxidized flavodoxin + 1-Hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0570-7970000000-9e120133948f567c4eb3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-008a-3910000000-5dcada1fca7c8514646aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9100000000-744acdeec7f0eb28fcd0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00e9-0890000000-f1627213072237479c59View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01vo-5790000000-47b787782b958bd69d50View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00b9-9400000000-7b8b6f0443210e85ef1eView 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
  • 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 ID18425
HMDB IDNot Available
Pubchem Compound ID21605869
Kegg IDC11453
ChemSpider ID10241147
Wikipedia IDNot Available
BioCyc ID2C-METH-D-ERYTHRITOL-CYCLODIPHOSPHATE
EcoCyc ID2C-METH-D-ERYTHRITOL-CYCLODIPHOSPHATE

Enzymes

Protein Details
• 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
General function:
Involved in 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
Specific function:
Converts 4-diphosphocytidyl-2-C-methyl-D-erythritol 2- phosphate into 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) and CMP. Also converts 4-diphosphocytidyl-2-C-methyl-D- erythritol into 2-C-methyl-D-erythritol 3,4-cyclophosphate and CMP
Gene Name:
ispF
Locus Tag:
PA3627
Molecular weight:
16.7 kDa
Reactions
2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP.
Protein Details
• 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
General function:
Involved in catalytic activity
Specific function:
Converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4cPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate
Gene Name:
ispG
Locus Tag:
PA3803
Molecular weight:
40.1 kDa
Reactions
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + H(2)O + 2 oxidized ferredoxin = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + 2 reduced ferredoxin.