MiMeDB: Showing metabocard for isoepoxydon (MMDBc0056045)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:14:08 UTC

Update Date

2022-08-12 20:09:33 UTC

Metabolite ID

MMDBc0056045

Metabolite Identification

Common Name

isoepoxydon

Description

Isoepoxydon belongs to the class of organic compounds known as cyclohexenones. Cyclohexenones are compounds containing a cylohexenone moiety, which is a six-membered aliphatic ring that carries a ketone and has one endocyclic double bond. Isoepoxydon is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on Isoepoxydon.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222142D          

 14 15  0  0  1  0            999 V2000
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5724    2.8875    0.0000 O   0  0  0  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
    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
    1.0164    2.3645    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  3  2  1  0  0  0  0
  4  1  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
  8  2  1  0  0  0  0
  4  9  1  6  0  0  0
 10  5  2  0  0  0  0
 11  6  1  0  0  0  0
 11  7  1  0  0  0  0
  4 12  1  1  0  0  0
  6 13  1  6  0  0  0
  7 14  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0056045

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]12O[C@]1([H])[C@@]([H])(O)C=C(CO)C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H8O4/c8-2-3-1-4(9)6-7(11-6)5(3)10/h1,4,6-9H,2H2/t4-,6+,7-/m0/s1

> <INCHI_KEY>
VTLJDPHPVHSVGR-JHYUDYDFSA-N

> <FORMULA>
C7H8O4

> <MOLECULAR_WEIGHT>
156.137

> <EXACT_MASS>
156.042258738

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
14.16419431867837

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,5S,6R)-5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one

> <JCHEM_LOGP>
-1.1024650153333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.97752759158228

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.63076313085298

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8219917495965676

> <JCHEM_POLAR_SURFACE_AREA>
70.06

> <JCHEM_REFRACTIVITY>
36.023599999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,5S,6R)-5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one

> <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       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.668   3.850   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       6.668   5.390   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       4.001   5.390   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+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       1.897   4.414   0.000  0.00  0.00           H+0
CONECT    1    3    4                                                       
CONECT    2    3    8                                                       
CONECT    3    1    2    5                                                  
CONECT    4    1    6    9   12                                             
CONECT    5    3    7   10                                                  
CONECT    6    4    7   11   13                                             
CONECT    7    5    6   11   14                                             
CONECT    8    2                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    6    7                                                       
CONECT   12    4                                                            
CONECT   13    6                                                            
CONECT   14    7                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

Synonyms

Value	Source
(1R,5S,6R)-5-Hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one	ChEBI
5,6-Epoxy-4-hydroxy-2-hydroxymethylcyclohex-2- en-1-one	MeSH

Molecular Formula

C₇H₈O₄

Average Mass

156.137

Monoisotopic Mass

156.042258738

IUPAC Name

(1R,5S,6R)-5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one

Traditional Name

(1R,5S,6R)-5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one

CAS Registry Number

Not Available

SMILES

[H][C@@]12O[C@]1([H])[C@@]([H])(O)C=C(CO)C2=O

InChI Identifier

InChI=1S/C7H8O4/c8-2-3-1-4(9)6-7(11-6)5(3)10/h1,4,6-9H,2H2/t4-,6+,7-/m0/s1

InChI Key

VTLJDPHPVHSVGR-JHYUDYDFSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclohexenones. Cyclohexenones are compounds containing a cylohexenone moiety, which is a six-membered aliphatic ring that carries a ketone and has one endocyclic double bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Cyclohexenones

Alternative Parents

Substituents

Cyclohexenone
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Ether
Oxirane
Dialkyl ether
Organic oxide
Hydrocarbon derivative
Primary alcohol
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
logP	-1.1	ChemAxon
pKa (Strongest Acidic)	13.63	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	70.06 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	36.02 m³·mol⁻¹	ChemAxon
Polarizability	14.16 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-09	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	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
MMDBr0017186	isoepoxydon	Hydrogen Ion	Isoepoxydon dehydrogenase patN	Dehydrogenation	RHEA	34755880
MMDBr0017187	isoepoxydon	Hydrogen Ion	Isoepoxydon dehydrogenase patN	Dehydrogenation	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
Eukaryota/Fungi	Ascomycota	2	Human feces; Human supragingival plaque

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

C00044399

Chemspider ID

293929

KEGG Compound ID

Not Available

BioCyc ID

CPD-16723

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

331736

PDB ID

Not Available

ChEBI ID

145109

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 isoepoxydon (MMDBc0056045)

MOL for #<Metabolite:0x00007fd0f45e4f58>

3D MOL for #<Metabolite:0x00007fd0f45e4f58>

3D SDF for #<Metabolite:0x00007fd0f45e4f58>

3D-SDF for #<Metabolite:0x00007fd0f45e4f58>

PDB for #<Metabolite:0x00007fd0f45e4f58>

3D PDB for #<Metabolite:0x00007fd0f45e4f58>

SMILES for #<Metabolite:0x00007fd0f45e4f58>

INCHI for #<Metabolite:0x00007fd0f45e4f58>

Structure for #<Metabolite:0x00007fd0f45e4f58>

3D Structure for #<Metabolite:0x00007fd0f45e4f58>