MiMeDB: Showing metabocard for 2-C-methyl-D-erythritol 3,4-cyclophosphate (MMDBc0055212)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:46:28 UTC

Update Date

2022-08-12 20:09:17 UTC

Metabolite ID

MMDBc0055212

Metabolite Identification

Common Name

2-C-methyl-D-erythritol 3,4-cyclophosphate

Description

Based on a literature review very few articles have been published on CHEBI:177365.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221462D          

 13 13  0  0  1  0            999 V2000
    1.3928    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    2.7643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2822    3.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2572    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2415   -0.9757    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.6517   -0.3268    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1673    1.4888    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  0  0  0  0
  4  5  1  1  0  0  0
  6  3  1  0  0  0  0
  5  7  1  6  0  0  0
 10  2  1  0  0  0  0
 11  4  1  0  0  0  0
 12  8  1  0  0  0  0
 12  9  2  0  0  0  0
 12 10  1  0  0  0  0
 12 11  1  0  0  0  0
  4 13  1  6  0  0  0
M  CHG  1   8  -1
M  END
> <DATABASE_ID>
MMDBc0055212

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(COP([O-])(=O)O1)[C@@](C)(O)CO

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O6P/c1-5(7,3-6)4-2-10-12(8,9)11-4/h4,6-7H,2-3H2,1H3,(H,8,9)/p-1/t4-,5+/m1/s1

> <INCHI_KEY>
BOPIGILYBRIHTQ-UHNVWZDZSA-M

> <FORMULA>
C5H10O6P

> <MOLECULAR_WEIGHT>
197.103

> <EXACT_MASS>
197.02204862

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
15.95920572277483

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R)-4-[(2S)-1,2-dihydroxypropan-2-yl]-2-oxo-1,3,2lambda5-dioxaphospholan-2-olate

> <JCHEM_LOGP>
-1.4158005363333332

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.197242595316222

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.833709985634718

> <JCHEM_PKA_STRONGEST_BASIC>
-3.105701853167292

> <JCHEM_POLAR_SURFACE_AREA>
99.05000000000001

> <JCHEM_REFRACTIVITY>
37.089

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(4R)-4-[(2S)-1,2-dihydroxypropan-2-yl]-2-oxo-1,3,2lambda5-dioxaphospholan-2-olate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       2.600   3.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.060   5.160   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.393   5.930   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -0.480   3.620   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.451  -1.821   0.000  0.00  0.00           O-1
HETATM    9  O   UNK     0      -1.217  -0.610   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.830  -0.290   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -0.186   1.175   0.000  0.00  0.00           O+0
HETATM   12  P   UNK     0       0.290  -0.290   0.000  0.00  0.00           P+0
HETATM   13  H   UNK     0      -0.312   2.779   0.000  0.00  0.00           H+0
CONECT    1    5                                                            
CONECT    2    4   10                                                       
CONECT    3    5    6                                                       
CONECT    4    2    5   11   13                                             
CONECT    5    1    3    4    7                                             
CONECT    6    3                                                            
CONECT    7    5                                                            
CONECT    8   12                                                            
CONECT    9   12                                                            
CONECT   10    2   12                                                       
CONECT   11    4   12                                                       
CONECT   12    8    9   10   11                                             
CONECT   13    4                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

Synonyms

Not Available

Molecular Formula

C₅H₁₀O₆P

Average Mass

197.103

Monoisotopic Mass

197.02204862

IUPAC Name

(4R)-4-[(2S)-1,2-dihydroxypropan-2-yl]-2-oxo-1,3,2lambda5-dioxaphospholan-2-olate

Traditional Name

(4R)-4-[(2S)-1,2-dihydroxypropan-2-yl]-2-oxo-1,3,2lambda5-dioxaphospholan-2-olate

CAS Registry Number

Not Available

SMILES

[H][C@@]1(COP([O-])(=O)O1)[C@@](C)(O)CO

InChI Identifier

InChI=1S/C5H11O6P/c1-5(7,3-6)4-2-10-12(8,9)11-4/h4,6-7H,2-3H2,1H3,(H,8,9)/p-1/t4-,5+/m1/s1

InChI Key

BOPIGILYBRIHTQ-UHNVWZDZSA-M

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-1.4	ChemAxon
pKa (Strongest Acidic)	1.83	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	99.05 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	37.09 m³·mol⁻¹	ChemAxon
Polarizability	15.96 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	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	View Spectrum

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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0017745	4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol	2-C-methyl-D-erythritol 3,4-cyclophosphate	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	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	Proteobacteria	1

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

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

156587264

PDB ID

Not Available

ChEBI ID

177365

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

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 3,4-cyclophosphate (MMDBc0055212)

MOL for #<Metabolite:0x00007fa4b461ee40>

3D MOL for #<Metabolite:0x00007fa4b461ee40>

3D SDF for #<Metabolite:0x00007fa4b461ee40>

3D-SDF for #<Metabolite:0x00007fa4b461ee40>

PDB for #<Metabolite:0x00007fa4b461ee40>

3D PDB for #<Metabolite:0x00007fa4b461ee40>

SMILES for #<Metabolite:0x00007fa4b461ee40>

INCHI for #<Metabolite:0x00007fa4b461ee40>

Structure for #<Metabolite:0x00007fa4b461ee40>

3D Structure for #<Metabolite:0x00007fa4b461ee40>