MiMeDB: Showing metabocard for (1R,2S,3R,4S,5S)-2,3-epoxy-5-methylcyclohexane-1,4-diol (MMDBc0016392)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 07:03:06 UTC

Update Date

2025-10-07 16:06:33 UTC

Metabolite ID

MMDBc0016392

Metabolite Identification

Common Name

(1R,2S,3R,4S,5S)-2,3-epoxy-5-methylcyclohexane-1,4-diol

Description

(1R,2S,3R,4S,5S)-2,3-epoxy-5-methylcyclohexane-1,4-diol is a cyclic diol compound belonging to the class of epoxy alcohols. There is limited literature available on this metabolite, indicating that further research is needed to fully understand its properties and biological significance.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152109032D          

 15 16  0  0  1  0            999 V2000
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164    2.3645    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  1  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  7  6  1  0  0  0  0
  4  8  1  1  0  0  0
  5  9  1  6  0  0  0
 10  6  1  0  0  0  0
 10  7  1  0  0  0  0
  3 11  1  6  0  0  0
  4 12  1  6  0  0  0
  5 13  1  6  0  0  0
  6 14  1  1  0  0  0
  7 15  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0016392

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]12O[C@]1([H])[C@@]([H])(O)[C@@]([H])(C)C[C@@]2([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C7H12O3/c1-3-2-4(8)6-7(10-6)5(3)9/h3-9H,2H2,1H3/t3-,4+,5-,6-,7+/m0/s1

> <INCHI_KEY>
CMZGQDPCPWKPGY-MLKOFDEISA-N

> <FORMULA>
C7H12O3

> <MOLECULAR_WEIGHT>
144.17

> <EXACT_MASS>
144.078644246

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
14.550847010157781

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2S,3S,5R,6S)-3-methyl-7-oxabicyclo[4.1.0]heptane-2,5-diol

> <ALOGPS_LOGP>
-0.68

> <JCHEM_LOGP>
-0.41734095933333293

> <ALOGPS_LOGS>
0.65

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.313074467467914

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.66863596660258

> <JCHEM_PKA_STRONGEST_BASIC>
-3.193226383145986

> <JCHEM_POLAR_SURFACE_AREA>
52.989999999999995

> <JCHEM_REFRACTIVITY>
34.3215

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.39e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,3S,5R,6S)-3-methyl-7-oxabicyclo[4.1.0]heptane-2,5-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335   3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   3.080   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.001   5.390   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM   11  H   UNK     0       5.335   4.620   0.000  0.00  0.00           H+0
HETATM   12  H   UNK     0       2.667   0.000   0.000  0.00  0.00           H+0
HETATM   13  H   UNK     0       4.001   2.310   0.000  0.00  0.00           H+0
HETATM   14  H   UNK     0       1.334   0.770   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       1.897   4.414   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2    3    4                                                       
CONECT    3    1    2    5   11                                             
CONECT    4    2    6    8   12                                             
CONECT    5    3    7    9   13                                             
CONECT    6    4    7   10   14                                             
CONECT    7    5    6   10   15                                             
CONECT    8    4                                                            
CONECT    9    5                                                            
CONECT   10    6    7                                                       
CONECT   11    3                                                            
CONECT   12    4                                                            
CONECT   13    5                                                            
CONECT   14    6                                                            
CONECT   15    7                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

Synonyms

Not Available

Molecular Formula

C₇H₁₂O₃

Average Mass

144.17

Monoisotopic Mass

144.078644246

IUPAC Name

(1R,2S,3S,5R,6S)-3-methyl-7-oxabicyclo[4.1.0]heptane-2,5-diol

Traditional Name

(1R,2S,3S,5R,6S)-3-methyl-7-oxabicyclo[4.1.0]heptane-2,5-diol

CAS Registry Number

Not Available

SMILES

[H][C@@]12O[C@]1([H])[C@@]([H])(O)[C@@]([H])(C)C[C@@]2([H])O

InChI Identifier

InChI=1S/C7H12O3/c1-3-2-4(8)6-7(10-6)5(3)9/h3-9H,2H2,1H3/t3-,4+,5-,6-,7+/m0/s1

InChI Key

CMZGQDPCPWKPGY-MLKOFDEISA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oxepanes. Oxepanes are compounds containing an oxepane ring, which is a seven-member saturated aliphatic heterocycle with one oxygen and six carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Oxepanes

Sub Class

Not Available

Direct Parent

Oxepanes

Alternative Parents

Substituents

Oxepane
Cyclic alcohol
Secondary alcohol
Oxacycle
Ether
Oxirane
Dialkyl ether
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	639 g/L	ALOGPS
logP	-0.68	ALOGPS
logP	-0.42	ChemAxon
logS	0.65	ALOGPS
pKa (Strongest Acidic)	13.67	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	52.99 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	34.32 m³·mol⁻¹	ChemAxon
Polarizability	14.55 Å³	ChemAxon
Number of Rings	2	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

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
Eukaryota/Fungi	Ascomycota	2	Human feces; Human sputum; Human	Metabolic reconstruction

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

30819426

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

73349167

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for (1R,2S,3R,4S,5S)-2,3-epoxy-5-methylcyclohexane-1,4-diol (MMDBc0016392)

MOL for #<Metabolite:0x00007f8dc4298138>

3D MOL for #<Metabolite:0x00007f8dc4298138>

3D SDF for #<Metabolite:0x00007f8dc4298138>

3D-SDF for #<Metabolite:0x00007f8dc4298138>

PDB for #<Metabolite:0x00007f8dc4298138>

3D PDB for #<Metabolite:0x00007f8dc4298138>

SMILES for #<Metabolite:0x00007f8dc4298138>

INCHI for #<Metabolite:0x00007f8dc4298138>

Structure for #<Metabolite:0x00007f8dc4298138>

3D Structure for #<Metabolite:0x00007f8dc4298138>