P. aeruginosa Metabolome Database: 2-C-Methyl-D-erythritol 2,4-cyclodiphosphate (PAMDB003502)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 11:54:54 AM

Metabolite ID

PAMDB003502

Identification

Name:

2-C-Methyl-D-erythritol 2,4-cyclodiphosphate

Description:

2-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

🔍MOL SDF PDB SMILES InChI View Structure

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

Average Molecular Weight:

278.0909

Monoisotopic Molecular Weight:

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-1,3,5,2???4???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

Taxonomy Description

This 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 Class

Organooxygen compounds

Class

Organic oxoanionic compounds

Sub Class

Organic pyrophosphates

Direct Parent

Organic pyrophosphates

Alternative Parents

Substituents

Organic pyrophosphate
Organic phosphoric acid derivative
Organic phosphate
Secondary alcohol
Polyol
Oxacycle
Organoheterocyclic compound
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

tetritol phosphate (CHEBI:18425 )

Physical Properties

State:

Not Available

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	21.4 mg/mL	ALOGPS
logP	-0.81	ALOGPS
logP	-1.8	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	1.83	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	142.75 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	49.08 m³·mol^-1	ChemAxon
Polarizability	20.4 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

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

Pathways:

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01ti-6980000000-2910078abdb147fc13f7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00ea-4910000000-25d3520582e8fc1a1eee	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9200000000-9aca2f6aa5f425257fca	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-0390000000-1b1435063fd721a5b41e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01u3-9440000000-28575060d57d85ca486c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9430000000-7e6056ba6fc2cfd9c792	View in MoNA

References

References:

Not Available

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	18425
HMDB ID	Not Available
Pubchem Compound ID	126747
Kegg ID	C11453
ChemSpider ID	112576
Wikipedia ID	Not Available
BioCyc ID	Not Available
Ligand Expo	CDI

2-C-Methyl-D-erythritol 2,4-cyclodiphosphate (PAMDB003502)

Structure for 2-C-Methyl-D-erythritol 2,4-cyclodiphosphate (PAMDB003502)