MiMeDB: Showing metabocard for 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate (MMDBc0029792)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:41:50 UTC

Update Date

2022-08-31 17:17:14 UTC

Metabolite ID

MMDBc0029792

Metabolite Identification

Common Name

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

Description

2-c-methyl-D-erythritol-2,4-cyclodiphosphate is a member of the chemical class known as Organic Pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652303072020242D          

 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  5  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  5  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  CHG  2   8  -1  10  -1
M  END
> <DATABASE_ID>
MMDBc0029792

> <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)/p-2/t4-,5+/m1/s1

> <INCHI_KEY>
SFRQRNJMIIUYDI-UHNVWZDZSA-L

> <FORMULA>
C5H10O9P2

> <MOLECULAR_WEIGHT>
276.075

> <EXACT_MASS>
275.980004942

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
19.845481956852463

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(6S,7R)-7-hydroxy-6-(hydroxymethyl)-6-methyl-2,4-dioxo-1,3,5,2lambda5,4lambda5-trioxadiphosphocane-2,4-bis(olate)

> <ALOGPS_LOGP>
-1.01

> <JCHEM_LOGP>
-1.8375990153333333

> <ALOGPS_LOGS>
-0.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2425208105265866

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8252549025773765

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1252726743191577

> <JCHEM_POLAR_SURFACE_AREA>
148.40999999999997

> <JCHEM_REFRACTIVITY>
46.8402

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.46e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(6S,7R)-7-hydroxy-6-(hydroxymethyl)-6-methyl-2,4-dioxo-1,3,5,2lambda5,4lambda5-trioxadiphosphocane-2,4-bis(olate)

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-MAR-20         0                                  
HETATM    1  C   UNK     0       0.235   3.720   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.282   2.193   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.091   2.394   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.859   2.782   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.436   2.193   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.680   3.817   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       1.859   4.322   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.809  -0.854   0.000  0.00  0.00           O-1
HETATM    9  O   UNK     0       3.483  -2.180   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -1.091  -0.854   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0       0.235  -2.180   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       3.871   0.770   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -0.153   0.770   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       1.859  -1.242   0.000  0.00  0.00           O+0
HETATM   15  P   UNK     0       3.282  -0.653   0.000  0.00  0.00           P+0
HETATM   16  P   UNK     0       0.436  -0.653   0.000  0.00  0.00           P+0
HETATM   17  H   UNK     0       3.139   3.638   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-cyclic diphosphate	ChEBI
2-C-Methyl-D-erythritol 2,4-cyclic diphosphate dianion	ChEBI
2-C-Methyl-D-erythritol 2,4-cyclic diphosphoric acid	Generator
2-C-Methyl-D-erythritol 2,4-cyclic diphosphoric acid dianion	Generator
2-C-Methyl-D-erythritol-2,4-cyclodiphosphoric acid	Generator

Molecular Formula

C₅H₁₀O₉P₂

Average Mass

276.075

Monoisotopic Mass

275.980004942

IUPAC Name

(6S,7R)-7-hydroxy-6-(hydroxymethyl)-6-methyl-2,4-dioxo-1,3,5,2lambda5,4lambda5-trioxadiphosphocane-2,4-bis(olate)

Traditional Name

(6S,7R)-7-hydroxy-6-(hydroxymethyl)-6-methyl-2,4-dioxo-1,3,5,2lambda5,4lambda5-trioxadiphosphocane-2,4-bis(olate)

CAS Registry Number

143488-44-2

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)/p-2/t4-,5+/m1/s1

InChI Key

SFRQRNJMIIUYDI-UHNVWZDZSA-L

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
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
Organic anion
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

organophosphate oxoanion (CHEBI:58483 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	54.6 g/L	ALOGPS
logP	-1	ALOGPS
logP	-1.8	ChemAxon
logS	-0.76	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	2	ChemAxon
Polar Surface Area	148.41 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	46.84 m³·mol⁻¹	ChemAxon
Polarizability	19.85 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

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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
MMDBr0018655	2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol	Cytidine monophosphate	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	Synthesis	PathBank	31602464
MMDBr0018656	2-C-Methyl-D-erythritol-2,4-cyclodiphosphate	1-Hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate	4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin)	Synthesis	PathBank	31602464
MMDBr0024807	di-mu-Sulfido-diiron(2+)	di-mu-Sulfido-diiron(1+)	4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (ferredoxin)	Synthesis	RHEA	34755880

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/Eubacteria	Proteobacteria	360	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Rat ; Sheep ; Pig ; Lion ; Cattle ; Turkey ; Dog ; Chicken	Unknown
Bacteria/Eubacteria	Actinobacteria	49	Human feces; Human ; Cattle
Bacteria/Eubacteria	Firmicutes	76	Human ; Human feces; Catfish
Bacteria/Eubacteria	Spirochaetes	9	Human ; Pig
Bacteria/Eubacteria	Cyanobacteria	14
Bacteria/Eubacteria	Verrucomicrobia	1	Human ; Human feces
Bacteria/Eubacteria	Aquificae	4
Bacteria/Eubacteria	Bacteroidetes	10	Human ; Human feces
Bacteria/Eubacteria	Chlamydiae	10	Human ; Sheep ; Cat
Bacteria/Eubacteria	Chlorobi	10
Bacteria/Eubacteria	Chloroflexi	3
Bacteria/Eubacteria	Deinococcus-thermus	4
Bacteria	Proteobacteria	4	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Rat ; Sheep ; Pig ; Lion ; Cattle ; Turkey ; Dog ; Chicken	Unknown
Bacteria/Eubacteria	Elusimicrobia	1
Bacteria/Eubacteria	Fusobacteria	1	Human ; Human feces
Bacteria/Eubacteria	Gemmatimonadetes	1
Bacteria/Eubacteria	Acidobacteria	2
Bacteria/Eubacteria	Thermotogae	8
Bacteria/Eubacteria	Tenericutes	2	Human
Bacteria/Eubacteria	Planctomycetes	1
Bacteria	nah	1
Bacteria/Eubacteria	Nitrospirae	1

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

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

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

METLIN ID

Not Available

PubChem Compound

21605869

PDB ID

Not Available

ChEBI ID

58483

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate (MMDBc0029792)

MOL for #<Metabolite:0x00007f923788d6c0>

3D MOL for #<Metabolite:0x00007f923788d6c0>

3D SDF for #<Metabolite:0x00007f923788d6c0>

3D-SDF for #<Metabolite:0x00007f923788d6c0>

PDB for #<Metabolite:0x00007f923788d6c0>

3D PDB for #<Metabolite:0x00007f923788d6c0>

SMILES for #<Metabolite:0x00007f923788d6c0>

INCHI for #<Metabolite:0x00007f923788d6c0>

Structure for #<Metabolite:0x00007f923788d6c0>

3D Structure for #<Metabolite:0x00007f923788d6c0>