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

Pharmaceutical

Xenobiotic

Record Information

Version

2.0

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

Not Available

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

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Not Available

Spectra

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-23	625.4
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	506.8
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-23	72.8
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	251.8
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	294.5
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	329.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	519.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	744.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	1064.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	181.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	228.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	190.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	24.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	624.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	771.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	71.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	360.0
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	778.6
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	644.3

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_1	C[C@@]1(CO)OP(=O)(O)OP(=O)(O)OC[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1730.34
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_2	C[C@@]1(CO[Si](C)(C)C)OP(=O)(O)OP(=O)(O)OC[C@H]1O	standard non polar	2025-10-24	1936.73
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_3	C[C@@]1(CO)OP(=O)(O)OP(=O)(O[Si](C)(C)C)OC[C@H]1O	standard non polar	2025-10-24	1893.59
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_4	C[C@@]1(CO)OP(=O)(O[Si](C)(C)C)OP(=O)(O)OC[C@H]1O	standard non polar	2025-10-24	1920.85
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_5	C[C@@]1(CO[Si](C)(C)C)OP(=O)(O)OP(=O)(O)OC[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1744.55
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_6	C[C@@]1(CO)OP(=O)(O[Si](C)(C)C)OP(=O)(O)OC[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1709.65
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_7	C[C@@]1(CO)OP(=O)(O)OP(=O)(O[Si](C)(C)C)OC[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1298.13
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_8	C[C@@]1(CO[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)OP(=O)(O)OC[C@H]1O	standard non polar	2025-10-24	2011.75
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_9	C[C@@]1(CO[Si](C)(C)C)OP(=O)(O)OP(=O)(O[Si](C)(C)C)OC[C@H]1O	standard non polar	2025-10-24	1449.94
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_10	C[C@@]1(CO)OP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)OC[C@H]1O	standard non polar	2025-10-24	2015.65
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_11	C[C@@]1(CO[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)OP(=O)(O)OC[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1876.99
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_12	C[C@@]1(CO[Si](C)(C)C)OP(=O)(O)OP(=O)(O[Si](C)(C)C)OC[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	2069.28
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_13	C[C@@]1(CO)OP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)OC[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	2151.38
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_14	C[C@@]1(CO[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)OC[C@H]1O	standard non polar	2025-10-24	2212.88
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_15	C[C@@]1(CO[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)OC[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1626.66
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_1	C[C@@]1(CO)OP(=O)(O)OP(=O)(O)OC[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	2014.4
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_2	C[C@@]1(CO[Si](C)(C)C)OP(=O)(O)OP(=O)(O)OC[C@H]1O	standard polar	2025-10-24	2559.0
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_3	C[C@@]1(CO)OP(=O)(O)OP(=O)(O[Si](C)(C)C)OC[C@H]1O	standard polar	2025-10-24	2073.21
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_4	C[C@@]1(CO)OP(=O)(O[Si](C)(C)C)OP(=O)(O)OC[C@H]1O	standard polar	2025-10-24	1726.3
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_5	C[C@@]1(CO[Si](C)(C)C)OP(=O)(O)OP(=O)(O)OC[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	1856.04
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_6	C[C@@]1(CO)OP(=O)(O[Si](C)(C)C)OP(=O)(O)OC[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	2307.52
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_7	C[C@@]1(CO)OP(=O)(O)OP(=O)(O[Si](C)(C)C)OC[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	1842.09
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_8	C[C@@]1(CO[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)OP(=O)(O)OC[C@H]1O	standard polar	2025-10-24	2408.88
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_9	C[C@@]1(CO[Si](C)(C)C)OP(=O)(O)OP(=O)(O[Si](C)(C)C)OC[C@H]1O	standard polar	2025-10-24	2528.18
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_10	C[C@@]1(CO)OP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)OC[C@H]1O	standard polar	2025-10-24	1639.76
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_11	C[C@@]1(CO[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)OP(=O)(O)OC[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	2728.42
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_12	C[C@@]1(CO[Si](C)(C)C)OP(=O)(O)OP(=O)(O[Si](C)(C)C)OC[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	1682.39
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_13	C[C@@]1(CO)OP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)OC[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	893.748
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_14	C[C@@]1(CO[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)OC[C@H]1O	standard polar	2025-10-24	1544.49
Gas Chromatography	2-C-Methyl-D-erythritol 2,4-cyclodiphosphate_TMS_15	C[C@@]1(CO[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)OC[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	2428.5

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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	1	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	287	Human feces; Human pleural fluid plaque; Pig ; Human ; Cattle ; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	173	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	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/Eubacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	116	Human feces; Human appendix biopsy; Human ; Human saliva; Human gastric fluid; Human urine; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	19	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	4		Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Tenericutes	2	Human feces	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Drugs - Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	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

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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:0x00007f9acc94a840>

3D MOL for #<Metabolite:0x00007f9acc94a840>

3D SDF for #<Metabolite:0x00007f9acc94a840>

3D-SDF for #<Metabolite:0x00007f9acc94a840>

PDB for #<Metabolite:0x00007f9acc94a840>

3D PDB for #<Metabolite:0x00007f9acc94a840>

SMILES for #<Metabolite:0x00007f9acc94a840>

INCHI for #<Metabolite:0x00007f9acc94a840>

Structure for #<Metabolite:0x00007f9acc94a840>

3D Structure for #<Metabolite:0x00007f9acc94a840>