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Showing metabocard for Benzene oxide (HMDB0248977)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 03:26:28 UTC
Update Date2021-09-26 22:59:33 UTC
HMDB IDHMDB0248977
Secondary Accession NumbersNone
Metabolite Identification
Common NameBenzene oxide
Description7-oxabicyclo[4.1.0]hepta-2,4-diene, also known as arene oxide, belongs to the class of organic compounds known as epoxides. Epoxides are compounds containing a cyclic ether with three ring atoms(one oxygen and two carbon atoms). 7-oxabicyclo[4.1.0]hepta-2,4-diene is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on 7-oxabicyclo[4.1.0]hepta-2,4-diene. This compound has been identified in human blood as reported by (PMID: 31557052 ). Benzene oxide is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Benzene oxide is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0248977 (Benzene oxide)

 
  Mrv1533006081518212D          
 
  7  8  0  0  0  0            999 V2000
   13.5101  -10.0356    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5101   -9.2106    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2713   -9.6718    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.7937  -10.4518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7937   -8.8018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0888  -10.0356    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0888   -9.2106    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  4  6  2  0  0  0  0
  5  7  2  0  0  0  0
  2  3  1  0  0  0  0
  6  7  1  0  0  0  0
M  END
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3D MOL for HMDB0248977 (Benzene oxide)

HMDB0248977
     RDKit          3D
Benzene oxide
 13 14  0  0  0  0  0  0  0  0999 V2000
    1.2370    0.6711   -0.0627 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1026    1.3513   -0.0403 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1412    0.7575   -0.0928 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2098    0.0681    0.1140 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1698   -0.6803    0.2268 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0108   -1.3630    0.0365 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1957   -0.7819   -0.0757 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2024    1.2071   -0.0714 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2260    2.4932    0.0276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3844    0.9675   -1.3513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2821   -0.8440    1.5102 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0885   -2.5019   -0.0451 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1243   -1.3447   -0.1757 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  1  1  0
  5  3  1  0
  1  8  1  0
  2  9  1  0
  3 10  1  0
  5 11  1  0
  6 12  1  0
  7 13  1  0
M  END
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3D SDF for HMDB0248977 (Benzene oxide)

 
  Mrv1533006081518212D          
 
  7  8  0  0  0  0            999 V2000
   13.5101  -10.0356    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5101   -9.2106    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2713   -9.6718    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.7937  -10.4518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7937   -8.8018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0888  -10.0356    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0888   -9.2106    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  4  6  2  0  0  0  0
  5  7  2  0  0  0  0
  2  3  1  0  0  0  0
  6  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0248977

> <DATABASE_NAME>
hmdb

> <SMILES>
O1C2C=CC=CC12

> <INCHI_IDENTIFIER>
InChI=1S/C6H6O/c1-2-4-6-5(3-1)7-6/h1-6H

> <INCHI_KEY>
WDFZWSZNOFELJY-UHFFFAOYSA-N

> <FORMULA>
C6H6O

> <MOLECULAR_WEIGHT>
94.113

> <EXACT_MASS>
94.041864813

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
9.513426082944815

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
7-oxabicyclo[4.1.0]hepta-2,4-diene

> <ALOGPS_LOGP>
0.46

> <JCHEM_LOGP>
0.9554650349999997

> <ALOGPS_LOGS>
-0.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.262520310067365

> <JCHEM_POLAR_SURFACE_AREA>
9.23

> <JCHEM_REFRACTIVITY>
29.052100000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.08e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
arene oxide

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0248977 (Benzene oxide)

HMDB0248977
     RDKit          3D
Benzene oxide
 13 14  0  0  0  0  0  0  0  0999 V2000
    1.2370    0.6711   -0.0627 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1026    1.3513   -0.0403 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1412    0.7575   -0.0928 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2098    0.0681    0.1140 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1698   -0.6803    0.2268 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0108   -1.3630    0.0365 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1957   -0.7819   -0.0757 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2024    1.2071   -0.0714 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2260    2.4932    0.0276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3844    0.9675   -1.3513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2821   -0.8440    1.5102 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0885   -2.5019   -0.0451 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1243   -1.3447   -0.1757 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  1  1  0
  5  3  1  0
  1  8  1  0
  2  9  1  0
  3 10  1  0
  5 11  1  0
  6 12  1  0
  7 13  1  0
M  END
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PDB for HMDB0248977 (Benzene oxide)

HEADER    PROTEIN                                 08-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-JUN-15         0                                  
HETATM    1  C   UNK     0      25.219 -18.733   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      25.219 -17.193   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      26.640 -18.054   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      23.882 -19.510   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      23.882 -16.430   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      22.566 -18.733   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      22.566 -17.193   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    3                                                  
CONECT    3    1    2                                                       
CONECT    4    1    6                                                       
CONECT    5    2    7                                                       
CONECT    6    4    7                                                       
CONECT    7    5    6                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   16    0
END
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3D PDB for HMDB0248977 (Benzene oxide)

COMPND    HMDB0248977
HETATM    1  C1  UNL     1       1.237   0.671  -0.063  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.103   1.351  -0.040  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.141   0.758  -0.093  1.00  0.00           C  
HETATM    4  O1  UNL     1      -2.210   0.068   0.114  1.00  0.00           O  
HETATM    5  C4  UNL     1      -1.170  -0.680   0.227  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.011  -1.363   0.036  1.00  0.00           C  
HETATM    7  C6  UNL     1       1.196  -0.782  -0.076  1.00  0.00           C  
HETATM    8  H1  UNL     1       2.202   1.207  -0.071  1.00  0.00           H  
HETATM    9  H2  UNL     1       0.226   2.493   0.028  1.00  0.00           H  
HETATM   10  H3  UNL     1      -1.384   0.968  -1.351  1.00  0.00           H  
HETATM   11  H4  UNL     1      -1.282  -0.844   1.510  1.00  0.00           H  
HETATM   12  H5  UNL     1       0.089  -2.502  -0.045  1.00  0.00           H  
HETATM   13  H6  UNL     1       2.124  -1.345  -0.176  1.00  0.00           H  
CONECT    1    2    2    7    8
CONECT    2    3    9
CONECT    3    4    5   10
CONECT    4    5
CONECT    5    6   11
CONECT    6    7    7   12
CONECT    7   13
END
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SMILES for HMDB0248977 (Benzene oxide)

O1C2C=CC=CC12
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INCHI for HMDB0248977 (Benzene oxide)

InChI=1S/C6H6O/c1-2-4-6-5(3-1)7-6/h1-6H
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Arene oxideKegg
Benzene oxideMeSH
Benzene oxide, conjugate acidMeSH
Chemical FormulaC6H6O
Average Molecular Weight94.113
Monoisotopic Molecular Weight94.041864813
IUPAC Name7-oxabicyclo[4.1.0]hepta-2,4-diene
Traditional Namearene oxide
CAS Registry NumberNot Available
SMILES
O1C2C=CC=CC12
InChI Identifier
InChI=1S/C6H6O/c1-2-4-6-5(3-1)7-6/h1-6H
InChI KeyWDFZWSZNOFELJY-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as epoxides. Epoxides are compounds containing a cyclic ether with three ring atoms(one oxygen and two carbon atoms).
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassEpoxides
Sub ClassNot Available
Direct ParentEpoxides
Alternative Parents
Substituents
  • Oxacycle
  • Ether
  • Oxirane
  • Dialkyl ether
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP0.46ALOGPS
logP0.96ChemAxon
logS-0.94ALOGPS
pKa (Strongest Basic)-4.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area9.23 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity29.05 m³·mol⁻¹ChemAxon
Polarizability9.51 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M-2H]-154.76730932474
DeepCCS[M+Na]+129.3830932474
AllCCS[M+H]+119.932859911
AllCCS[M+H-H2O]+114.732859911
AllCCS[M+NH4]+124.732859911
AllCCS[M+Na]+126.132859911
AllCCS[M-H]-114.832859911
AllCCS[M+Na-2H]-117.232859911
AllCCS[M+HCOO]-119.932859911

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Benzene oxide GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9000000000-ac0d2076c7ca0ac6bbcb2021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Benzene oxide GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Benzene oxide GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Benzene oxide 10V, Positive-QTOFsplash10-0002-9000000000-88958a184bdcd9f462242021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Benzene oxide 20V, Positive-QTOFsplash10-0002-9000000000-88958a184bdcd9f462242021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Benzene oxide 40V, Positive-QTOFsplash10-0002-9000000000-e9ac19613a0379856ab52021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Benzene oxide 10V, Negative-QTOFsplash10-0006-9000000000-08485aaf085c13d5129a2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Benzene oxide 20V, Negative-QTOFsplash10-0006-9000000000-08485aaf085c13d5129a2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Benzene oxide 40V, Negative-QTOFsplash10-0006-9000000000-08485aaf085c13d5129a2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID94703
KEGG Compound IDC01782
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]