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

2022-08-31 18:24:27 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


  Mrv0541 10101211172D          

 17 17  0  0  0  0            999 V2000
    0.1260    1.9926    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7581    1.1747    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5843    1.2824    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9959    1.4904    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2337    1.1747    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9000    2.0446    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9959    2.3154    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5760   -0.4574    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8657   -1.1676    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5843   -0.4574    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1260   -1.1676    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0738    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0821    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9959   -0.6654    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7581   -0.3497    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.2337   -0.3497    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.6818    1.9488    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  6  0  0  0
  5  3  1  1  0  0  0
  5  4  1  0  0  0  0
  6  3  1  0  0  0  0
  4  7  1  6  0  0  0
 12  2  1  0  0  0  0
 13  5  1  0  0  0  0
 15  8  1  0  0  0  0
 15  9  2  0  0  0  0
 15 12  1  0  0  0  0
 15 14  1  0  0  0  0
 16 10  1  0  0  0  0
 16 11  2  0  0  0  0
 16 13  1  0  0  0  0
 16 14  1  0  0  0  0
  4 17  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031762

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(O)COP(O)(=O)OP(O)(=O)O[C@@]1(C)CO

> <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

> <FORMULA>
C5H12O9P2

> <MOLECULAR_WEIGHT>
278.0909

> <EXACT_MASS>
277.995655006

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
20.40042368881135

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(6S,7R)-2,4,7-trihydroxy-6-(hydroxymethyl)-6-methyl-1,3,5,2λ⁵,4λ⁵-trioxadiphosphocane-2,4-dione

> <ALOGPS_LOGP>
-0.81

> <JCHEM_LOGP>
-1.8375990153333333

> <ALOGPS_LOGS>
-1.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2225208105292085

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8252549025773765

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1252726743191577

> <JCHEM_POLAR_SURFACE_AREA>
142.75

> <JCHEM_REFRACTIVITY>
49.083600000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.14e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-mthbcp

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-OCT-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   15  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   16  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   17  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    5                                                            
CONECT    2    4   12                                                       
CONECT    3    5    6                                                       
CONECT    4    2    5    7   17                                             
CONECT    5    1    3    4   13                                             
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8   15                                                            
CONECT    9   15                                                            
CONECT   10   16                                                            
CONECT   11   16                                                            
CONECT   12    2   15                                                       
CONECT   13    5   16                                                       
CONECT   14   15   16                                                       
CONECT   15    8    9   12   14                                             
CONECT   16   10   11   13   14                                             
CONECT   17    4                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

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

(6S,7R)-2,4,7-trihydroxy-6-(hydroxymethyl)-6-methyl-1,3,5,2λ⁵,4λ⁵-trioxadiphosphocane-2,4-dione

Traditional Name

3-mthbcp

CAS Registry Number

Not Available

SMILES

[H][C@@]1(O)COP(O)(=O)OP(O)(=O)O[C@@]1(C)CO

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

Property	Value	Source
Water Solubility	21.4 g/L	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	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01ti-6980000000-2910078abdb147fc13f7	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00ea-4910000000-25d3520582e8fc1a1eee	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9200000000-9aca2f6aa5f425257fca	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-0390000000-1b1435063fd721a5b41e	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01u3-9440000000-28575060d57d85ca486c	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9430000000-7e6056ba6fc2cfd9c792	2015-09-15	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum

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

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	2C-methyl-D-erythritol 2,4 cyclodiphosphate dehydratase	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	Source Sub-type	Species	Data Source	Reference

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:0x00007f5a8d0644d0>

3D MOL for #<Metabolite:0x00007f5a8d0644d0>

3D SDF for #<Metabolite:0x00007f5a8d0644d0>

3D-SDF for #<Metabolite:0x00007f5a8d0644d0>

PDB for #<Metabolite:0x00007f5a8d0644d0>

3D PDB for #<Metabolite:0x00007f5a8d0644d0>

SMILES for #<Metabolite:0x00007f5a8d0644d0>

INCHI for #<Metabolite:0x00007f5a8d0644d0>

Structure for #<Metabolite:0x00007f5a8d0644d0>

3D Structure for #<Metabolite:0x00007f5a8d0644d0>