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Showing metabocard for o-Xylene (HMDB0059851)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2013-03-07 21:32:59 UTC
Update Date2022-03-07 03:17:37 UTC
HMDB IDHMDB0059851
Secondary Accession Numbers
  • HMDB59851
Metabolite Identification
Common Nameo-Xylene
Descriptiono-Xylene, also known as O-dimethylbenzene or O-methyltoluene, belongs to the class of organic compounds known as o-xylenes. These are aromatic compounds that contain a o-xylene moiety, which is a monocyclic benzene carrying exactly two methyl groups at the 1- and 2-positions. o-Xylene is possibly neutral. o-Xylene is a geranium tasting compound. Outside of the human body, o-Xylene is found, on average, in the highest concentration within black walnuts. o-Xylene has also been detected, but not quantified in, several different foods, such as sweet cherries, cucumbers, evergreen blackberries, corns, and cauliflowers. This could make O-xylene a potential biomarker for the consumption of these foods. o-Xylene is a potentially toxic compound.
Structure
Data?1563865983
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0059851 (o-Xylene)

  Mrv1652303202018592D          

  8  8  0  0  0  0            999 V2000
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
M  END
Download

3D MOL for HMDB0059851 (o-Xylene)

HMDB0059851
     RDKit          3D
o-Xylene
 18 18  0  0  0  0  0  0  0  0999 V2000
   -1.6793    1.2335   -0.0472 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2881    0.7137   -0.0284 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8203    1.5122   -0.0598 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0770    0.9319   -0.0386 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2367   -0.4536    0.0142 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1109   -1.2504    0.0456 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1342   -0.6564    0.0239 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3155   -1.5644    0.0596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6992    2.3346   -0.1888 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1710    0.9384    0.9222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2187    0.7408   -0.8619 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6798    2.5845   -0.1008 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9640    1.5616   -0.0635 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2373   -0.8736    0.0295 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2142   -2.3276    0.0868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2617   -1.0416    0.2164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4032   -2.1136   -0.9199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1690   -2.2702    0.9106 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  7  2  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
  6 15  1  0
  8 16  1  0
  8 17  1  0
  8 18  1  0
M  END
Download

3D SDF for HMDB0059851 (o-Xylene)

  Mrv1652303202018592D          

  8  8  0  0  0  0            999 V2000
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0059851

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CC=CC=C1C

> <INCHI_IDENTIFIER>
InChI=1S/C8H10/c1-7-5-3-4-6-8(7)2/h3-6H,1-2H3

> <INCHI_KEY>
CTQNGGLPUBDAKN-UHFFFAOYSA-N

> <FORMULA>
C8H10

> <MOLECULAR_WEIGHT>
106.165

> <EXACT_MASS>
106.07825032

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.963866913466479

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,2-xylene

> <ALOGPS_LOGP>
3.16

> <JCHEM_LOGP>
3.000088594666667

> <ALOGPS_LOGS>
-2.71

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
36.1404

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.05e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ortho-xylene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0059851 (o-Xylene)

HMDB0059851
     RDKit          3D
o-Xylene
 18 18  0  0  0  0  0  0  0  0999 V2000
   -1.6793    1.2335   -0.0472 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2881    0.7137   -0.0284 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8203    1.5122   -0.0598 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0770    0.9319   -0.0386 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2367   -0.4536    0.0142 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1109   -1.2504    0.0456 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1342   -0.6564    0.0239 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3155   -1.5644    0.0596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6992    2.3346   -0.1888 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1710    0.9384    0.9222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2187    0.7408   -0.8619 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6798    2.5845   -0.1008 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9640    1.5616   -0.0635 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2373   -0.8736    0.0295 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2142   -2.3276    0.0868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2617   -1.0416    0.2164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4032   -2.1136   -0.9199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1690   -2.2702    0.9106 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  7  2  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
  6 15  1  0
  8 16  1  0
  8 17  1  0
  8 18  1  0
M  END
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PDB for HMDB0059851 (o-Xylene)

HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2    8                                                  
CONECT    8    7                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0059851 (o-Xylene)

COMPND    HMDB0059851
HETATM    1  C1  UNL     1      -1.679   1.234  -0.047  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.288   0.714  -0.028  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.820   1.512  -0.060  1.00  0.00           C  
HETATM    4  C4  UNL     1       2.077   0.932  -0.039  1.00  0.00           C  
HETATM    5  C5  UNL     1       2.237  -0.454   0.014  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.111  -1.250   0.046  1.00  0.00           C  
HETATM    7  C7  UNL     1      -0.134  -0.656   0.024  1.00  0.00           C  
HETATM    8  C8  UNL     1      -1.315  -1.564   0.060  1.00  0.00           C  
HETATM    9  H1  UNL     1      -1.699   2.335  -0.189  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.171   0.938   0.922  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.219   0.741  -0.862  1.00  0.00           H  
HETATM   12  H4  UNL     1       0.680   2.585  -0.101  1.00  0.00           H  
HETATM   13  H5  UNL     1       2.964   1.562  -0.063  1.00  0.00           H  
HETATM   14  H6  UNL     1       3.237  -0.874   0.030  1.00  0.00           H  
HETATM   15  H7  UNL     1       1.214  -2.328   0.087  1.00  0.00           H  
HETATM   16  H8  UNL     1      -2.262  -1.042   0.216  1.00  0.00           H  
HETATM   17  H9  UNL     1      -1.403  -2.114  -0.920  1.00  0.00           H  
HETATM   18  H10 UNL     1      -1.169  -2.270   0.911  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3    3    7
CONECT    3    4   12
CONECT    4    5    5   13
CONECT    5    6   14
CONECT    6    7    7   15
CONECT    7    8
CONECT    8   16   17   18
END
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SMILES for HMDB0059851 (o-Xylene)

CC1=CC=CC=C1C
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INCHI for HMDB0059851 (o-Xylene)

InChI=1S/C8H10/c1-7-5-3-4-6-8(7)2/h3-6H,1-2H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1,2-DimethylbenzeneChEBI
1,2-DimethylbenzolChEBI
2-XyleneChEBI
3,4-XyleneChEBI
O-DimethylbenzeneChEBI
O-MethyltolueneChEBI
O-XylolChEBI
ORTHO-xyleneChEBI
1,2-XyleneHMDB
Chemical FormulaC8H10
Average Molecular Weight106.165
Monoisotopic Molecular Weight106.07825032
IUPAC Name1,2-xylene
Traditional Nameortho-xylene
CAS Registry NumberNot Available
SMILES
CC1=CC=CC=C1C
InChI Identifier
InChI=1S/C8H10/c1-7-5-3-4-6-8(7)2/h3-6H,1-2H3
InChI KeyCTQNGGLPUBDAKN-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as o-xylenes. These are aromatic compounds that contain a o-xylene moiety, which is a monocyclic benzene carrying exactly two methyl groups at the 1- and 2-positions.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassXylenes
Direct Parento-Xylenes
Alternative Parents
Substituents
  • O-xylene
  • Aromatic hydrocarbon
  • Unsaturated hydrocarbon
  • Hydrocarbon
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
Role
Industrial application
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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen Locations
  • Blood
  • Feces
  • Saliva
Tissue LocationsNot Available
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Ulcerative colitis
  1. Garner CE, Smith S, de Lacy Costello B, White P, Spencer R, Probert CS, Ratcliffe NM: Volatile organic compounds from feces and their potential for diagnosis of gastrointestinal disease. FASEB J. 2007 Jun;21(8):1675-88. Epub 2007 Feb 21. [PubMed:17314143 ]
Nonalcoholic fatty liver disease
  1. Raman M, Ahmed I, Gillevet PM, Probert CS, Ratcliffe NM, Smith S, Greenwood R, Sikaroodi M, Lam V, Crotty P, Bailey J, Myers RP, Rioux KP: Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease. Clin Gastroenterol Hepatol. 2013 Jul;11(7):868-75.e1-3. doi: 10.1016/j.cgh.2013.02.015. Epub 2013 Feb 27. [PubMed:23454028 ]
Autism
  1. De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, Cristofori F, Guerzoni ME, Gobbetti M, Francavilla R: Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS One. 2013 Oct 9;8(10):e76993. doi: 10.1371/journal.pone.0076993. eCollection 2013. [PubMed:24130822 ]
Pervasive developmental disorder not otherwise specified
  1. De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, Cristofori F, Guerzoni ME, Gobbetti M, Francavilla R: Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS One. 2013 Oct 9;8(10):e76993. doi: 10.1371/journal.pone.0076993. eCollection 2013. [PubMed:24130822 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB005819
KNApSAcK IDNot Available
Chemspider ID6967
KEGG Compound IDC07212
BioCyc IDCPD-1421
BiGG IDNot Available
Wikipedia LinkO-Xylene
METLIN IDNot Available
PubChem Compound7237
PDB IDNot Available
ChEBI ID28063
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00029813
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Han QJ, Wu HL, Cai CB, Tang LJ, Yu RQ: Using near-infrared spectroscopy and differential adsorption bed method to study adsorption kinetics of orthoxylene on silica gel. Talanta. 2008 Aug 15;76(4):752-7. doi: 10.1016/j.talanta.2008.04.021. Epub 2008 Apr 20. [PubMed:18656653 ]
  2. Silaev MM: [New kinetic model of the radical-chain oxidation, including competitive reactions: oxygen as an autoinhibitor]. Biofizika. 2001 Mar-Apr;46(2):203-9. [PubMed:11357330 ]
  3. van Beelen P, Fleuren-Kemila AK: Toxic effects of pentachlorophenol and other pollutants on the mineralization of acetate in several soils. Ecotoxicol Environ Saf. 1993 Aug;26(1):10-7. [PubMed:7691530 ]