Hmdb loader

Showing metabocard for 3,4-Dimethylthiophene (HMDB0032980)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 17:53:04 UTC
Update Date2023-02-21 17:22:55 UTC
HMDB IDHMDB0032980
Secondary Accession Numbers
  • HMDB32980
Metabolite Identification
Common Name3,4-Dimethylthiophene
Description3,4-Dimethylthiophene 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. 3,4-Dimethylthiophene has been detected, but not quantified in, garden onions (Allium cepa). This could make 3,4-dimethylthiophene a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on 3,4-Dimethylthiophene.
Structure
Data?1677000175
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0032980 (3,4-Dimethylthiophene)


  Mrv0541 05061306502D          

  7  7  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
   -0.8843    0.8843    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
    0.1553   -0.1553    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
   -0.0997    0.6294    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
  5  1  1  0  0  0  0
  5  3  2  0  0  0  0
  6  2  1  0  0  0  0
  6  4  2  0  0  0  0
  6  5  1  0  0  0  0
  7  3  1  0  0  0  0
  7  4  1  0  0  0  0
M  END
Download

3D MOL for HMDB0032980 (3,4-Dimethylthiophene)

HMDB0032980
     RDKit          3D
3,4-Dimethylthiophene
 15 15  0  0  0  0  0  0  0  0999 V2000
   -1.5335   -0.9263    0.1994 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6683    0.3021   -0.0160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2700    1.5270   -0.1644 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0530    2.5824   -0.3754 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.3246    1.4395   -0.2689 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6637    0.2528   -0.0690 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4941   -1.0086    0.0743 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4078   -0.6720    0.8242 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8310   -1.3026   -0.7807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9600   -1.6875    0.7643 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3501    1.7613   -0.1493 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4064    1.6429   -0.3469 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9128   -0.9942    1.0896 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8927   -1.9048   -0.0608 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2735   -1.0121   -0.7203 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  1  0
  5  6  2  0
  6  7  1  0
  6  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  5 12  1  0
  7 13  1  0
  7 14  1  0
  7 15  1  0
M  END
Download

3D SDF for HMDB0032980 (3,4-Dimethylthiophene)


  Mrv0541 05061306502D          

  7  7  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
   -0.8843    0.8843    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
    0.1553   -0.1553    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
   -0.0997    0.6294    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
  5  1  1  0  0  0  0
  5  3  2  0  0  0  0
  6  2  1  0  0  0  0
  6  4  2  0  0  0  0
  6  5  1  0  0  0  0
  7  3  1  0  0  0  0
  7  4  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0032980

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CSC=C1C

> <INCHI_IDENTIFIER>
InChI=1S/C6H8S/c1-5-3-7-4-6(5)2/h3-4H,1-2H3

> <INCHI_KEY>
GPSFYJDZKSRMKZ-UHFFFAOYSA-N

> <FORMULA>
C6H8S

> <MOLECULAR_WEIGHT>
112.193

> <EXACT_MASS>
112.034670946

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
12.683693120591858

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,4-dimethylthiophene

> <ALOGPS_LOGP>
2.69

> <JCHEM_LOGP>
2.780530547666667

> <ALOGPS_LOGS>
-2.31

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.574081826301711

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
33.2462

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.44e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,4-dimethylthiophene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0032980 (3,4-Dimethylthiophene)

HMDB0032980
     RDKit          3D
3,4-Dimethylthiophene
 15 15  0  0  0  0  0  0  0  0999 V2000
   -1.5335   -0.9263    0.1994 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6683    0.3021   -0.0160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2700    1.5270   -0.1644 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0530    2.5824   -0.3754 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.3246    1.4395   -0.2689 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6637    0.2528   -0.0690 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4941   -1.0086    0.0743 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4078   -0.6720    0.8242 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8310   -1.3026   -0.7807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9600   -1.6875    0.7643 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3501    1.7613   -0.1493 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4064    1.6429   -0.3469 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9128   -0.9942    1.0896 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8927   -1.9048   -0.0608 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2735   -1.0121   -0.7203 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  1  0
  5  6  2  0
  6  7  1  0
  6  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  5 12  1  0
  7 13  1  0
  7 14  1  0
  7 15  1  0
M  END
Download

PDB for HMDB0032980 (3,4-Dimethylthiophene)

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      -1.651   1.651   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.290  -0.290   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  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    7  S   UNK     0       1.830  -0.290   0.000  0.00  0.00           S+0
CONECT    1    5                                                            
CONECT    2    6                                                            
CONECT    3    5    7                                                       
CONECT    4    6    7                                                       
CONECT    5    1    3    6                                                  
CONECT    6    2    4    5                                                  
CONECT    7    3    4                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
Download

3D PDB for HMDB0032980 (3,4-Dimethylthiophene)

COMPND    HMDB0032980
HETATM    1  C1  UNL     1      -1.534  -0.926   0.199  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.668   0.302  -0.016  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.270   1.527  -0.164  1.00  0.00           C  
HETATM    4  S1  UNL     1       0.053   2.582  -0.375  1.00  0.00           S  
HETATM    5  C4  UNL     1       1.325   1.439  -0.269  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.664   0.253  -0.069  1.00  0.00           C  
HETATM    7  C6  UNL     1       1.494  -1.009   0.074  1.00  0.00           C  
HETATM    8  H1  UNL     1      -2.408  -0.672   0.824  1.00  0.00           H  
HETATM    9  H2  UNL     1      -1.831  -1.303  -0.781  1.00  0.00           H  
HETATM   10  H3  UNL     1      -0.960  -1.687   0.764  1.00  0.00           H  
HETATM   11  H4  UNL     1      -2.350   1.761  -0.149  1.00  0.00           H  
HETATM   12  H5  UNL     1       2.406   1.643  -0.347  1.00  0.00           H  
HETATM   13  H6  UNL     1       1.913  -0.994   1.090  1.00  0.00           H  
HETATM   14  H7  UNL     1       0.893  -1.905  -0.061  1.00  0.00           H  
HETATM   15  H8  UNL     1       2.273  -1.012  -0.720  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    3    6
CONECT    3    4   11
CONECT    4    5
CONECT    5    6    6   12
CONECT    6    7
CONECT    7   13   14   15
END
Download

SMILES for HMDB0032980 (3,4-Dimethylthiophene)

CC1=CSC=C1C
Download

INCHI for HMDB0032980 (3,4-Dimethylthiophene)

InChI=1S/C6H8S/c1-5-3-7-4-6(5)2/h3-4H,1-2H3
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
3,4-Dimethyl-thiopheneHMDB
Chemical FormulaC6H8S
Average Molecular Weight112.193
Monoisotopic Molecular Weight112.034670946
IUPAC Name3,4-dimethylthiophene
Traditional Name3,4-dimethylthiophene
CAS Registry Number632-15-5
SMILES
CC1=CSC=C1C
InChI Identifier
InChI=1S/C6H8S/c1-5-3-7-4-6(5)2/h3-4H,1-2H3
InChI KeyGPSFYJDZKSRMKZ-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
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point144.00 to 146.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility351.5 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP2.551 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.54 g/LALOGPS
logP2.69ALOGPS
logP2.78ChemAxon
logS-2.3ALOGPS
pKa (Strongest Basic)-6.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity33.25 m³·mol⁻¹ChemAxon
Polarizability12.68 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]+118.93631661259
DarkChem[M-H]-113.32731661259
DeepCCS[M+H]+122.57330932474
DeepCCS[M-H]-120.57630932474
DeepCCS[M-2H]-156.40630932474
DeepCCS[M+Na]+130.97530932474
AllCCS[M+H]+117.732859911
AllCCS[M+H-H2O]+112.732859911
AllCCS[M+NH4]+122.332859911
AllCCS[M+Na]+123.632859911
AllCCS[M-H]-119.332859911
AllCCS[M+Na-2H]-122.432859911
AllCCS[M+HCOO]-125.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3,4-DimethylthiopheneCC1=CSC=C1C1251.3Standard polar33892256
3,4-DimethylthiopheneCC1=CSC=C1C879.6Standard non polar33892256
3,4-DimethylthiopheneCC1=CSC=C1C898.7Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3,4-Dimethylthiophene GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-6900000000-90ef9f380fdc17b6fb5a2016-09-22Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4-Dimethylthiophene GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4-Dimethylthiophene 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 - 3,4-Dimethylthiophene 10V, Positive-QTOFsplash10-03di-0900000000-9f1c794c2d71bca466832016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,4-Dimethylthiophene 20V, Positive-QTOFsplash10-03di-0900000000-5de3987810196b4450bd2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,4-Dimethylthiophene 40V, Positive-QTOFsplash10-0udi-9100000000-b307e1263a686bd382232016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,4-Dimethylthiophene 10V, Negative-QTOFsplash10-03di-0900000000-94dddff22e6c2bddfc1d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,4-Dimethylthiophene 20V, Negative-QTOFsplash10-03di-3900000000-0f8fb9b83046603956bd2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,4-Dimethylthiophene 40V, Negative-QTOFsplash10-00di-9100000000-2386f78574575bb63b3c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,4-Dimethylthiophene 10V, Positive-QTOFsplash10-03di-2900000000-1a61bfa174ddaa0c83602021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,4-Dimethylthiophene 20V, Positive-QTOFsplash10-03y0-9300000000-2f224fa2645fd6d8ac132021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,4-Dimethylthiophene 40V, Positive-QTOFsplash10-014i-9000000000-d80c96b53c5b6a361b652021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,4-Dimethylthiophene 10V, Negative-QTOFsplash10-03di-0900000000-0b420ab7e14ab10017dc2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,4-Dimethylthiophene 20V, Negative-QTOFsplash10-03di-3900000000-a94daba21f05267746d92021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,4-Dimethylthiophene 40V, Negative-QTOFsplash10-0229-9700000000-98b05b1155b8970a6d652021-09-22Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Membrane
Biospecimen Locations
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
UrineDetected 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 IDFDB010967
KNApSAcK IDC00052140
Chemspider ID71421
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound79089
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1574431
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.. .