2-C-Methyl-D-erythritol 2,4-cyclodiphosphate (ECMDB23112) (M2MDB003502)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (2)
Record Information
Version2.0
Creation Date2012-10-10 12:17:09 -0600
Update Date2015-06-03 17:25:57 -0600
Secondary Accession Numbers
  • ECMDB23112
Identification
Name:2-C-Methyl-D-erythritol 2,4-cyclodiphosphate
Description2-C-Methyl-D-erythritol 2,4-cyclodiphosphate or MECDP is a highly unusual cyclodiphosphate-containing intermediate in the mevalonate-independent pathway to isopentenyl diphosphate and dimethylallyl diphosphate (i.e. isoprenoid biosynthesis). It is a product of the enzyme 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase which catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to MECDP [PMID: 11786530]
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • (6S,7R)-2,4-dihydroxy-6-(hydroxymethyl)-6-methyl-2,4-dioxo-1,3,5,2$l^{5},4$l^{5}-trioxadiphosphocan-7-ol
  • (6S,7R)-6-(Hydroxymethyl)-6-methyl-1,3,5,2,4-trioxadiphosphocane-2,4,7-triol 2,4-dioxide
  • 2-C-Methyl-D-erythritol 2,4-cyclodiphosphoric acid
  • 3-Methyl-1,2,3,4-tetrahydroxybutane-1,3-cyclic bisphosphate
  • 3-Methyl-1,2,3,4-tetrahydroxybutane-1,3-cyclic bisphosphoric acid
Chemical Formula:C5H12O9P2
Weight:Average: 278.0909
Monoisotopic: 277.995655006
InChI Key:SFRQRNJMIIUYDI-UHNVWZDZSA-N
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)/t4-,5+/m1/s1
CAS number:Not Available
IUPAC Name:(6S,7R)-2,4,7-trihydroxy-6-(hydroxymethyl)-6-methyl-1,3,5,2λ⁵,4λ⁵-trioxadiphosphocane-2,4-dione
Traditional IUPAC Name:3-mthbcp
SMILES:[H][C@@]1(O)COP(O)(=O)OP(O)(=O)O[C@@]1(C)CO
Chemical Taxonomy
Description 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.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganic oxoanionic compounds
Sub ClassOrganic pyrophosphates
Direct ParentOrganic pyrophosphates
Alternative Parents
Substituents
  • Organic pyrophosphate
  • Organic phosphoric acid derivative
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility21.4 g/LALOGPS
logP-0.81ALOGPS
logP-1.8ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)1.83ChemAxon
pKa (Strongest Basic)-3.1ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area142.75 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity49.08 m³·mol⁻¹ChemAxon
Polarizability20.4 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
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
1-Hydroxy-2-methyl-2-butenyl 4-diphosphate + Water + 2 oxidized ferredoxin > 2-C-Methyl-D-erythritol 2,4-cyclodiphosphate +2 reduced ferredoxin
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
SMPDB Pathways:Not Available
KEGG Pathways:Not Available
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-01ti-6980000000-2910078abdb147fc13f7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00ea-4910000000-25d3520582e8fc1a1eeeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9200000000-9aca2f6aa5f425257fcaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0390000000-1b1435063fd721a5b41eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01u3-9440000000-28575060d57d85ca486cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9430000000-7e6056ba6fc2cfd9c792View in MoNA
MSMass Spectrum (Electron Ionization)Not AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:Not Available
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID18425
HMDB IDNot Available
Pubchem Compound ID126747
Kegg IDC11453
ChemSpider IDNot Available
Wikipedia ID2-C-Methyl-D-erythritol-2,4-cyclopyrophosphate
BioCyc IDNot Available
Ligand ExpoCDI

Enzymes

Protein Details
1. 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
Uniprot ID:
P62617
Molecular weight:
16897
Reactions
2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP.
Protein Details
2. 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
Uniprot ID:
P62620
Molecular weight:
40683
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.