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Showing metabocard for m-Xylene (HMDB0059810)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2013-03-07 21:30:43 UTC
Update Date2021-09-07 17:05:38 UTC
HMDB IDHMDB0059810
Secondary Accession Numbers
  • HMDB59810
Metabolite Identification
Common Namem-Xylene
Descriptionm-Xylene, also known as 1,3-xylene or m-dimethylbenzene, belongs to the class of organic compounds known as m-xylenes. These are aromatic compounds that contain a m-xylene moiety, which is a monocyclic benzene carrying exactly two methyl groups at the 1- and 3-positions. The conversion m-xylene to isophthalic acid entails catalytic oxidation. m-Xylene (meta-xylene) is an aromatic hydrocarbon. m-Xylene is possibly neutral. m-Xylene is a plastic tasting compound. m-xylene is found, on average, in the highest concentration in safflowers. m-xylene has also been detected, but not quantified, in black walnuts and parsley. This could make m-xylene a potential biomarker for the consumption of these foods. Xylenes are not acutely toxic, for example the LD50 (rat, oral) is 4300 mg/kg. m-Xylene is a potentially toxic compound. Concerns with xylenes focus on narcotic effects. The m- stands for meta-, indicating that the two methyl groups in m-xylene occupy positions 1 and 3 on a benzene ring. All xylene isomers are colorless and highly flammable. Petroleum contains about 1 weight percent xylenes.
Structure
Data?1563865977
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0059810 (m-Xylene)


  Mrv1652303202019002D          

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

3D MOL for HMDB0059810 (m-Xylene)

HMDB0059810
     RDKit          3D
m-Xylene
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.5110   -0.7836    0.3508 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2083   -0.1074    0.0771 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1403    1.1905   -0.3836 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0476    1.8361   -0.6434 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2402    1.1878   -0.4459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1946   -0.1152    0.0160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4579   -0.8431    0.2398 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0080   -0.7579    0.2752 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3315   -0.3426   -0.2599 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8134   -0.7211    1.4008 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4609   -1.8609    0.0232 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0906    1.7069   -0.5410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0892    2.8561   -1.0052 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2113    1.6459   -0.6337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7522   -0.8677    1.3038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3451   -1.8899   -0.1003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2755   -0.3470   -0.3142 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0497   -1.7869    0.6402 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  1  0
  6  8  2  0
  8  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
  7 15  1  0
  7 16  1  0
  7 17  1  0
  8 18  1  0
M  END
Download

3D SDF for HMDB0059810 (m-Xylene)


  Mrv1652303202019002D          

  8  8  0  0  0  0            999 V2000
    0.7145    2.0625    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
    1.4289    0.0000    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
    0.7145   -0.4125    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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  2  0  0  0  0
  5  3  1  0  0  0  0
  7  1  1  0  0  0  0
  7  4  1  0  0  0  0
  7  6  2  0  0  0  0
  8  2  1  0  0  0  0
  8  5  2  0  0  0  0
  8  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0059810

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CC(C)=CC=C1

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

> <INCHI_KEY>
IVSZLXZYQVIEFR-UHFFFAOYSA-N

> <FORMULA>
C8H10

> <MOLECULAR_WEIGHT>
106.165

> <EXACT_MASS>
106.07825032

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
13.085558841067837

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,3-xylene

> <ALOGPS_LOGP>
3.15

> <JCHEM_LOGP>
3.000088594666667

> <ALOGPS_LOGS>
-2.72

> <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>
2.03e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
M-xylene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0059810 (m-Xylene)

HMDB0059810
     RDKit          3D
m-Xylene
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.5110   -0.7836    0.3508 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2083   -0.1074    0.0771 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1403    1.1905   -0.3836 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0476    1.8361   -0.6434 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2402    1.1878   -0.4459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1946   -0.1152    0.0160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4579   -0.8431    0.2398 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0080   -0.7579    0.2752 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3315   -0.3426   -0.2599 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8134   -0.7211    1.4008 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4609   -1.8609    0.0232 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0906    1.7069   -0.5410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0892    2.8561   -1.0052 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2113    1.6459   -0.6337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7522   -0.8677    1.3038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3451   -1.8899   -0.1003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2755   -0.3470   -0.3142 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0497   -1.7869    0.6402 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  1  0
  6  8  2  0
  8  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
  7 15  1  0
  7 16  1  0
  7 17  1  0
  8 18  1  0
M  END
Download

PDB for HMDB0059810 (m-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       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -0.770   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       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   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       0.000   0.000   0.000  0.00  0.00           C+0
CONECT    1    7                                                            
CONECT    2    8                                                            
CONECT    3    4    5                                                       
CONECT    4    3    7                                                       
CONECT    5    3    8                                                       
CONECT    6    7    8                                                       
CONECT    7    1    4    6                                                  
CONECT    8    2    5    6                                                  
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
Download

3D PDB for HMDB0059810 (m-Xylene)

COMPND    HMDB0059810
HETATM    1  C1  UNL     1       2.511  -0.784   0.351  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.208  -0.107   0.077  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.140   1.191  -0.384  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.048   1.836  -0.643  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.240   1.188  -0.446  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.195  -0.115   0.016  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.458  -0.843   0.240  1.00  0.00           C  
HETATM    8  C8  UNL     1       0.008  -0.758   0.275  1.00  0.00           C  
HETATM    9  H1  UNL     1       3.332  -0.343  -0.260  1.00  0.00           H  
HETATM   10  H2  UNL     1       2.813  -0.721   1.401  1.00  0.00           H  
HETATM   11  H3  UNL     1       2.461  -1.861   0.023  1.00  0.00           H  
HETATM   12  H4  UNL     1       2.091   1.707  -0.541  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.089   2.856  -1.005  1.00  0.00           H  
HETATM   14  H6  UNL     1      -2.211   1.646  -0.634  1.00  0.00           H  
HETATM   15  H7  UNL     1      -2.752  -0.868   1.304  1.00  0.00           H  
HETATM   16  H8  UNL     1      -2.345  -1.890  -0.100  1.00  0.00           H  
HETATM   17  H9  UNL     1      -3.276  -0.347  -0.314  1.00  0.00           H  
HETATM   18  H10 UNL     1       0.050  -1.787   0.640  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3    3    8
CONECT    3    4   12
CONECT    4    5    5   13
CONECT    5    6   14
CONECT    6    7    8    8
CONECT    7   15   16   17
CONECT    8   18
END
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SMILES for HMDB0059810 (m-Xylene)

CC1=CC(C)=CC=C1
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INCHI for HMDB0059810 (m-Xylene)

InChI=1S/C8H10/c1-7-4-3-5-8(2)6-7/h3-6H,1-2H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1,3-DimethylbenzeneChEBI
1,3-DimethylbenzolChEBI
1,3-XyleneChEBI
3-XyleneChEBI
m-DimethylbenzeneChEBI
m-MethyltolueneChEBI
m-XylolChEBI
Meta-xyleneChEBI
Chemical FormulaC8H10
Average Molecular Weight106.165
Monoisotopic Molecular Weight106.07825032
IUPAC Name1,3-xylene
Traditional NameM-xylene
CAS Registry NumberNot Available
SMILES
CC1=CC(C)=CC=C1
InChI Identifier
InChI=1S/C8H10/c1-7-4-3-5-8(2)6-7/h3-6H,1-2H3
InChI KeyIVSZLXZYQVIEFR-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as m-xylenes. These are aromatic compounds that contain a m-xylene moiety, which is a monocyclic benzene carrying exactly two methyl groups at the 1- and 3-positions.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassXylenes
Direct Parentm-Xylenes
Alternative Parents
Substituents
  • M-xylene
  • Aromatic hydrocarbon
  • Unsaturated hydrocarbon
  • Hydrocarbon
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic 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
Water Solubility0.2 g/LALOGPS
logP3.15ALOGPS
logP3ChemAxon
logS-2.7ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity36.14 m³·mol⁻¹ChemAxon
Polarizability13.09 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+121.54831661259
DarkChem[M-H]-118.62231661259
DeepCCS[M+H]+125.02330932474
DeepCCS[M-H]-121.97530932474
DeepCCS[M-2H]-158.77230932474
DeepCCS[M+Na]+133.66830932474
AllCCS[M+H]+115.132859911
AllCCS[M+H-H2O]+110.032859911
AllCCS[M+NH4]+119.832859911
AllCCS[M+Na]+121.232859911
AllCCS[M-H]-116.632859911
AllCCS[M+Na-2H]-119.132859911
AllCCS[M+HCOO]-121.832859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.4.85 minutes32390414
Predicted by Siyang on May 30, 202216.1433 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20224.14 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1846.4 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid619.9 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid245.5 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid434.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid311.4 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid671.1 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid695.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)345.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1375.7 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid560.8 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1450.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid469.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid442.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate573.8 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA402.9 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water58.2 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
m-XyleneCC1=CC(C)=CC=C11146.3Standard polar33892256
m-XyleneCC1=CC(C)=CC=C1862.0Standard non polar33892256
m-XyleneCC1=CC(C)=CC=C1858.2Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen Locations
  • Blood
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.00129 (0.00120-0.00138) uMAdult (>18 years old)Not SpecifiedNormal
    • National Health a...
 details
BloodDetected and Quantified0.00111 (0.000989-0.00122) uMChildren (1-13 years old)Not SpecifiedNormal
    • National Health a...
 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Campylobacter jejuni infection		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Ulcerative Colitis		 details
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 ]
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB005816
KNApSAcK IDC00035778
Chemspider ID7641
KEGG Compound IDC07208
BioCyc IDMETA-XYLENE
BiGG IDNot Available
Wikipedia LinkM-xylene
METLIN IDNot Available
PubChem Compound7929
PDB IDNot Available
ChEBI ID28488
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. Wang DL, Chen CL, Zhao C, Gao J, Kong DY, You H, Brugger J: [The solution of nonlinear function of ion mobility based on FAIMS spectrum peak position]. Guang Pu Xue Yu Guang Pu Fen Xi. 2012 Aug;32(8):2050-5. [PubMed:23156750 ]