MiMeDB: Showing metabocard for 2-C-Methyl-D-erythritol 2,4-cyclodiphosphate (MMDBc0031762)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:48:19 UTC

Update Date

2024-10-13 14:07:36 UTC

Metabolite ID

MMDBc0031762

Metabolite Identification

Common 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

Synonyms

Value	Source
2-C-Methyl-D-erythritol 2,4-cyclodiphosphate	ChEBI
3-Methyl-1,2,3,4-tetrahydroxybutane-1,3-cyclic bisphosphate	ChEBI
MEcPP	ChEBI
2-C-Methyl-D-erythritol 2,4-cyclodiphosphoric acid	Generator
3-Methyl-1,2,3,4-tetrahydroxybutane-1,3-cyclic bisphosphoric acid	Generator
2C-Methyl-D-erythritol 2,4-cyclodiphosphoric acid	Generator
3-MTHBCP	MeSH
ME-2,4-cyclopp	MeSH
Methylerythritol cyclodiphosphate	MeSH
2C Methyl-D-erythritol 2,4-cyclodiphosphate	MeSH
MEcPP CPD	MeSH
Methyl-D-erythritol 2,4-cyclodiphosphate	MeSH
2C-m-ECP	MeSH

Molecular Formula

C₅H₁₂O₉P₂

Average Mass

278.0909

Monoisotopic Mass

277.995655006

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

Not Available

InChI Identifier

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

InChI Key

SFRQRNJMIIUYDI-UHNVWZDZSA-N

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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organic oxoanionic compounds

Sub Class

Organic pyrophosphates

Direct Parent

Organic 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 Framework

Aliphatic heteromonocyclic compounds

External Descriptors

tetritol phosphate (CHEBI:18425 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Not Available

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0007485	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate	1-Hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate	Not Available		VMH	30371894

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	174	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	287	Human feces; Human pleural fluid plaque; Pig ; Human ; Human stool; Cattle ; Human saliva	Metabolic reconstruction
Bacteria	Actinobacteria	119	Human feces; Human pleural fluid plaque; Human dental plaque; Human sputum; Human ; Human nasopharyngeal swab; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	116	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human gastric fluid; Human urine; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Bacteria	Synergistetes	3	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Fusobacteria	19	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	4		Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria	Tenericutes	2	Human feces	Metabolic reconstruction

Exposure Sources

Source Type	Activity	Data Source	Reference
Drugs	Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	Not Available	U.S. Environmental Protection Agency	CompTox
Domestics	Not Available	U.S. Environmental Protection Agency	CompTox

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

Not Available

DrugBank ID

DB03961

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00007295

Chemspider ID

Not Available

KEGG Compound ID

C11453

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

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

METLIN ID

Not Available

PubChem Compound

126747

PDB ID

Not Available

ChEBI ID

18425

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for 2-C-Methyl-D-erythritol 2,4-cyclodiphosphate (MMDBc0031762)

MOL for #<Metabolite:0x00007fdb19a35650>

3D MOL for #<Metabolite:0x00007fdb19a35650>

3D SDF for #<Metabolite:0x00007fdb19a35650>

3D-SDF for #<Metabolite:0x00007fdb19a35650>

PDB for #<Metabolite:0x00007fdb19a35650>

3D PDB for #<Metabolite:0x00007fdb19a35650>

SMILES for #<Metabolite:0x00007fdb19a35650>

INCHI for #<Metabolite:0x00007fdb19a35650>

Structure for #<Metabolite:0x00007fdb19a35650>

3D Structure for #<Metabolite:0x00007fdb19a35650>