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Showing metabocard for 3-Methylthiophene (HMDB0033119)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 17:53:50 UTC
Update Date2023-02-21 17:23:06 UTC
HMDB IDHMDB0033119
Secondary Accession Numbers
  • HMDB33119
Metabolite Identification
Common Name3-Methylthiophene
Description3-Methylthiophene belongs to the class of organic compounds known as heteroaromatic compounds. Heteroaromatic compounds are compounds containing an aromatic ring where a carbon atom is linked to an hetero atom. 3-Methylthiophene has been detected, but not quantified in, several different foods, such as arabica coffees (Coffea arabica), coffee and coffee products, guavas (Psidium guajava), and robusta coffees (Coffea canephora). This could make 3-methylthiophene a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 3-Methylthiophene.
Structure
Data?1677000186
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0033119 (3-Methylthiophene)


  Mrv0541 05061306562D          

  6  6  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  5  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  4  2  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
M  END
Download

3D MOL for HMDB0033119 (3-Methylthiophene)

HMDB0033119
     RDKit          3D
3-Methylthiophene
 12 12  0  0  0  0  0  0  0  0999 V2000
   -1.6790   -0.2384    0.0279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1958    0.1172    0.0293 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7758   -0.7914   -0.2043 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0660   -0.3459   -0.1748 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8972    1.3111    0.1740 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.1982    1.4041    0.2750 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1897    0.3155    0.8379 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8171   -1.3118    0.2311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1421    0.0788   -0.9237 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5686   -1.8677   -0.4157 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9773   -0.9468   -0.3423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4594    2.2753    0.4857 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  2  2  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  3 10  1  0
  4 11  1  0
  6 12  1  0
M  END
Download

3D SDF for HMDB0033119 (3-Methylthiophene)


  Mrv0541 05061306562D          

  6  6  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  5  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  4  2  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0033119

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CSC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C5H6S/c1-5-2-3-6-4-5/h2-4H,1H3

> <INCHI_KEY>
QENGPZGAWFQWCZ-UHFFFAOYSA-N

> <FORMULA>
C5H6S

> <MOLECULAR_WEIGHT>
98.166

> <EXACT_MASS>
98.019020882

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
10.678387484542592

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methylthiophene

> <ALOGPS_LOGP>
2.28

> <JCHEM_LOGP>
2.267109158333333

> <ALOGPS_LOGS>
-1.97

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.2088445991888825

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
28.205000000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.05e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-methylthiophene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0033119 (3-Methylthiophene)

HMDB0033119
     RDKit          3D
3-Methylthiophene
 12 12  0  0  0  0  0  0  0  0999 V2000
   -1.6790   -0.2384    0.0279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1958    0.1172    0.0293 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7758   -0.7914   -0.2043 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0660   -0.3459   -0.1748 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8972    1.3111    0.1740 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.1982    1.4041    0.2750 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1897    0.3155    0.8379 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8171   -1.3118    0.2311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1421    0.0788   -0.9237 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5686   -1.8677   -0.4157 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9773   -0.9468   -0.3423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4594    2.2753    0.4857 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  2  2  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  3 10  1  0
  4 11  1  0
  6 12  1  0
M  END
Download

PDB for HMDB0033119 (3-Methylthiophene)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    6  S   UNK     0       1.830  -0.290   0.000  0.00  0.00           S+0
CONECT    1    5                                                            
CONECT    2    3    5                                                       
CONECT    3    2    6                                                       
CONECT    4    5    6                                                       
CONECT    5    1    2    4                                                  
CONECT    6    3    4                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0033119 (3-Methylthiophene)

COMPND    HMDB0033119
HETATM    1  C1  UNL     1      -1.679  -0.238   0.028  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.196   0.117   0.029  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.776  -0.791  -0.204  1.00  0.00           C  
HETATM    4  C4  UNL     1       2.066  -0.346  -0.175  1.00  0.00           C  
HETATM    5  S1  UNL     1       1.897   1.311   0.174  1.00  0.00           S  
HETATM    6  C5  UNL     1       0.198   1.404   0.275  1.00  0.00           C  
HETATM    7  H1  UNL     1      -2.190   0.316   0.838  1.00  0.00           H  
HETATM    8  H2  UNL     1      -1.817  -1.312   0.231  1.00  0.00           H  
HETATM    9  H3  UNL     1      -2.142   0.079  -0.924  1.00  0.00           H  
HETATM   10  H4  UNL     1       0.569  -1.868  -0.416  1.00  0.00           H  
HETATM   11  H5  UNL     1       2.977  -0.947  -0.342  1.00  0.00           H  
HETATM   12  H6  UNL     1      -0.459   2.275   0.486  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3    6    6
CONECT    3    4    4   10
CONECT    4    5   11
CONECT    5    6
CONECT    6   12
END
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SMILES for HMDB0033119 (3-Methylthiophene)

CC1=CSC=C1
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INCHI for HMDB0033119 (3-Methylthiophene)

InChI=1S/C5H6S/c1-5-2-3-6-4-5/h2-4H,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
3-Methyl-thiopheneHMDB
3-ThiotoleneHMDB
b-ThiotoleneHMDB
beta-MethylthiopheneHMDB
Methyl-3-thiopheneHMDB
P3MTHMDB, MeSH
Poly(3-methylthiophene)HMDB, MeSH
Thiophene, 3-methyl-, homopolymerHMDB
Chemical FormulaC5H6S
Average Molecular Weight98.166
Monoisotopic Molecular Weight98.019020882
IUPAC Name3-methylthiophene
Traditional Name3-methylthiophene
CAS Registry Number616-44-4
SMILES
CC1=CSC=C1
InChI Identifier
InChI=1S/C5H6S/c1-5-2-3-6-4-5/h2-4H,1H3
InChI KeyQENGPZGAWFQWCZ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as heteroaromatic compounds. Heteroaromatic compounds are compounds containing an aromatic ring where a carbon atom is linked to an hetero atom.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassHeteroaromatic compounds
Sub ClassNot Available
Direct ParentHeteroaromatic compounds
Alternative Parents
Substituents
  • Heteroaromatic compound
  • Thiophene
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-69 °CNot Available
Boiling Point115.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility0.4 mg/mL at 25 °CNot Available
LogP2.34Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility1.05 g/LALOGPS
logP2.28ALOGPS
logP2.27ChemAxon
logS-2ALOGPS
pKa (Strongest Basic)-7.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity28.2 m³·mol⁻¹ChemAxon
Polarizability10.68 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]+115.23731661259
DarkChem[M-H]-107.91631661259
DeepCCS[M+H]+120.38330932474
DeepCCS[M-H]-118.11430932474
DeepCCS[M-2H]-154.00730932474
DeepCCS[M+Na]+128.66330932474
AllCCS[M+H]+114.832859911
AllCCS[M+H-H2O]+109.732859911
AllCCS[M+NH4]+119.632859911
AllCCS[M+Na]+121.032859911
AllCCS[M-H]-119.532859911
AllCCS[M+Na-2H]-123.232859911
AllCCS[M+HCOO]-127.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-MethylthiopheneCC1=CSC=C11107.6Standard polar33892256
3-MethylthiopheneCC1=CSC=C1756.9Standard non polar33892256
3-MethylthiopheneCC1=CSC=C1787.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Methylthiophene GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9000000000-5e550cb8f39a476ef95d2016-09-22Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Methylthiophene 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 - 3-Methylthiophene 10V, Positive-QTOFsplash10-0002-9000000000-7ad9d5fe18954f0835902016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylthiophene 20V, Positive-QTOFsplash10-0002-9000000000-f5921ba9485011d8c32c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylthiophene 40V, Positive-QTOFsplash10-0udj-9000000000-8539d10d3591334b1b362016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylthiophene 10V, Negative-QTOFsplash10-0002-9000000000-f4b710c29ddd5d4e425a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylthiophene 20V, Negative-QTOFsplash10-0002-9000000000-647b6b07246e3008c6c42016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylthiophene 40V, Negative-QTOFsplash10-0a4i-9000000000-d4e47d4ea28da443d39b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylthiophene 10V, Negative-QTOFsplash10-0002-9000000000-3cd398d06bc9c83555ad2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylthiophene 20V, Negative-QTOFsplash10-00xs-9000000000-acf640513beb3e9664e52021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylthiophene 40V, Negative-QTOFsplash10-0002-9000000000-b64cd6b3398f51a11cc62021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylthiophene 10V, Positive-QTOFsplash10-0002-9000000000-9679e65ae990f5ab77852021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylthiophene 20V, Positive-QTOFsplash10-052b-9000000000-488357da3c5eb31795e02021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylthiophene 40V, Positive-QTOFsplash10-0udi-9000000000-14e0c2238c95a109302c2021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen Locations
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Ulcerative colitis		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Crohn's disease 		details
Associated Disorders and Diseases
Disease References
Ulcerative colitis
  1. De Preter V, Machiels K, Joossens M, Arijs I, Matthys C, Vermeire S, Rutgeerts P, Verbeke K: Faecal metabolite profiling identifies medium-chain fatty acids as discriminating compounds in IBD. Gut. 2015 Mar;64(3):447-58. doi: 10.1136/gutjnl-2013-306423. Epub 2014 May 8. [PubMed:24811995 ]
Crohn's disease
  1. De Preter V, Machiels K, Joossens M, Arijs I, Matthys C, Vermeire S, Rutgeerts P, Verbeke K: Faecal metabolite profiling identifies medium-chain fatty acids as discriminating compounds in IBD. Gut. 2015 Mar;64(3):447-58. doi: 10.1136/gutjnl-2013-306423. Epub 2014 May 8. [PubMed:24811995 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB011119
KNApSAcK IDNot Available
Chemspider ID21111820
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link3-Methylthiophene
METLIN IDNot Available
PubChem Compound12024
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1192191
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .