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Showing metabocard for 5-Methyl-3-thiophenethiol (HMDB0039788)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 01:19:38 UTC
Update Date2023-02-21 17:27:09 UTC
HMDB IDHMDB0039788
Secondary Accession Numbers
  • HMDB39788
Metabolite Identification
Common Name5-Methyl-3-thiophenethiol
Description5-Methyl-3-thiophenethiol 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. Based on a literature review very few articles have been published on 5-Methyl-3-thiophenethiol.
Structure
Data?1677000429
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0039788 (5-Methyl-3-thiophenethiol)


  Mrv0541 05061311242D          

  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
    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
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  2  0  0  0  0
  5  2  1  0  0  0  0
  5  3  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 HMDB0039788 (5-Methyl-3-thiophenethiol)

HMDB0039788
     RDKit          3D
5-Methyl-3-thiophenethiol
 13 13  0  0  0  0  0  0  0  0999 V2000
   -2.3710   -0.1730    0.1580 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9140    0.2247    0.0982 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1467   -0.5281   -0.3313 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3577    0.0297   -0.2968 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8679   -0.8330   -0.8310 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.4495    1.3156    0.1664 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1704    1.6985    0.5384 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5384   -0.9088   -0.6387 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5451   -0.5666    1.1774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9720    0.7548    0.0299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0594   -1.5603   -0.6843 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4022   -1.4032    0.3401 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3465    1.9497    0.2738 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
  4  6  2  0
  6  7  1  0
  7  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  5 12  1  0
  6 13  1  0
M  END
Download

3D SDF for HMDB0039788 (5-Methyl-3-thiophenethiol)


  Mrv0541 05061311242D          

  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
    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
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  2  0  0  0  0
  5  2  1  0  0  0  0
  5  3  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>
HMDB0039788

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CC(S)=CS1

> <INCHI_IDENTIFIER>
InChI=1S/C5H6S2/c1-4-2-5(6)3-7-4/h2-3,6H,1H3

> <INCHI_KEY>
AKXPXNGITUAYOF-UHFFFAOYSA-N

> <FORMULA>
C5H6S2

> <MOLECULAR_WEIGHT>
130.231

> <EXACT_MASS>
129.991091572

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
13.751872633610642

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-methylthiophene-3-thiol

> <ALOGPS_LOGP>
2.52

> <JCHEM_LOGP>
2.492755758

> <ALOGPS_LOGS>
-2.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.379807941878165

> <JCHEM_PKA_STRONGEST_BASIC>
-7.406756780141146

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
36.2299

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.04e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-methylthiophene-3-thiol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0039788 (5-Methyl-3-thiophenethiol)

HMDB0039788
     RDKit          3D
5-Methyl-3-thiophenethiol
 13 13  0  0  0  0  0  0  0  0999 V2000
   -2.3710   -0.1730    0.1580 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9140    0.2247    0.0982 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1467   -0.5281   -0.3313 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3577    0.0297   -0.2968 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8679   -0.8330   -0.8310 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.4495    1.3156    0.1664 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1704    1.6985    0.5384 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5384   -0.9088   -0.6387 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5451   -0.5666    1.1774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9720    0.7548    0.0299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0594   -1.5603   -0.6843 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4022   -1.4032    0.3401 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3465    1.9497    0.2738 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
  4  6  2  0
  6  7  1  0
  7  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  5 12  1  0
  6 13  1  0
M  END
Download

PDB for HMDB0039788 (5-Methyl-3-thiophenethiol)

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       2.306   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       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    6  S   UNK     0       2.735  -1.536   0.000  0.00  0.00           S+0
HETATM    7  S   UNK     0      -0.186   1.175   0.000  0.00  0.00           S+0
CONECT    1    4                                                            
CONECT    2    4    5                                                       
CONECT    3    5    7                                                       
CONECT    4    1    2    7                                                  
CONECT    5    2    3    6                                                  
CONECT    6    5                                                            
CONECT    7    3    4                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0039788 (5-Methyl-3-thiophenethiol)

COMPND    HMDB0039788
HETATM    1  C1  UNL     1      -2.371  -0.173   0.158  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.914   0.225   0.098  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.147  -0.528  -0.331  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.358   0.030  -0.297  1.00  0.00           C  
HETATM    5  S1  UNL     1       2.868  -0.833  -0.831  1.00  0.00           S  
HETATM    6  C5  UNL     1       1.450   1.316   0.166  1.00  0.00           C  
HETATM    7  S2  UNL     1      -0.170   1.699   0.538  1.00  0.00           S  
HETATM    8  H1  UNL     1      -2.538  -0.909  -0.639  1.00  0.00           H  
HETATM    9  H2  UNL     1      -2.545  -0.567   1.177  1.00  0.00           H  
HETATM   10  H3  UNL     1      -2.972   0.755   0.030  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.059  -1.560  -0.684  1.00  0.00           H  
HETATM   12  H5  UNL     1       3.402  -1.403   0.340  1.00  0.00           H  
HETATM   13  H6  UNL     1       2.347   1.950   0.274  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    3    7
CONECT    3    4   11
CONECT    4    5    6    6
CONECT    5   12
CONECT    6    7   13
END
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SMILES for HMDB0039788 (5-Methyl-3-thiophenethiol)

CC1=CC(S)=CS1
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INCHI for HMDB0039788 (5-Methyl-3-thiophenethiol)

InChI=1S/C5H6S2/c1-4-2-5(6)3-7-4/h2-3,6H,1H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
3-mercapto-5-MethylthiopheneHMDB
Chemical FormulaC5H6S2
Average Molecular Weight130.231
Monoisotopic Molecular Weight129.991091572
IUPAC Name5-methylthiophene-3-thiol
Traditional Name5-methylthiophene-3-thiol
CAS Registry Number2634-17-5
SMILES
CC1=CC(S)=CS1
InChI Identifier
InChI=1S/C5H6S2/c1-4-2-5(6)3-7-4/h2-3,6H,1H3
InChI KeyAKXPXNGITUAYOF-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
  • Arylthiol
  • Hydrocarbon derivative
  • Organosulfur compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
Role
Biological role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility226.7 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.2 g/LALOGPS
logP2.52ALOGPS
logP2.49ChemAxon
logS-2.8ALOGPS
pKa (Strongest Acidic)6.38ChemAxon
pKa (Strongest Basic)-7.4ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity36.23 m³·mol⁻¹ChemAxon
Polarizability13.75 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]+122.42331661259
DarkChem[M-H]-118.27431661259
DeepCCS[M+H]+128.11830932474
DeepCCS[M-H]-126.13830932474
DeepCCS[M-2H]-162.08830932474
DeepCCS[M+Na]+136.65430932474
AllCCS[M+H]+121.232859911
AllCCS[M+H-H2O]+116.332859911
AllCCS[M+NH4]+125.632859911
AllCCS[M+Na]+126.932859911
AllCCS[M-H]-123.532859911
AllCCS[M+Na-2H]-126.632859911
AllCCS[M+HCOO]-130.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5-Methyl-3-thiophenethiolCC1=CC(S)=CS11654.9Standard polar33892256
5-Methyl-3-thiophenethiolCC1=CC(S)=CS11060.5Standard non polar33892256
5-Methyl-3-thiophenethiolCC1=CC(S)=CS11073.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
5-Methyl-3-thiophenethiol,1TMS,isomer #1CC1=CC(S[Si](C)(C)C)=CS11313.9Semi standard non polar33892256
5-Methyl-3-thiophenethiol,1TMS,isomer #1CC1=CC(S[Si](C)(C)C)=CS11272.5Standard non polar33892256
5-Methyl-3-thiophenethiol,1TBDMS,isomer #1CC1=CC(S[Si](C)(C)C(C)(C)C)=CS11586.3Semi standard non polar33892256
5-Methyl-3-thiophenethiol,1TBDMS,isomer #1CC1=CC(S[Si](C)(C)C(C)(C)C)=CS11541.0Standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 5-Methyl-3-thiophenethiol GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-9700000000-867b2a34b5787e89a7b72017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Methyl-3-thiophenethiol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Methyl-3-thiophenethiol 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 - 5-Methyl-3-thiophenethiol 10V, Positive-QTOFsplash10-001i-0900000000-ab39265ae31af57fd6cd2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-thiophenethiol 20V, Positive-QTOFsplash10-001i-6900000000-bce5e509ad53e55bbab82016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-thiophenethiol 40V, Positive-QTOFsplash10-0uei-9000000000-463fbe78a1eb508cdc7e2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-thiophenethiol 10V, Negative-QTOFsplash10-004i-0900000000-f38b93e15106d58254be2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-thiophenethiol 20V, Negative-QTOFsplash10-004i-4900000000-e66cb59606592fd126132016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-thiophenethiol 40V, Negative-QTOFsplash10-000i-9000000000-97fb30056a409637b1632016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-thiophenethiol 10V, Positive-QTOFsplash10-001i-4900000000-c9c7048d8b77d5c613e02021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-thiophenethiol 20V, Positive-QTOFsplash10-00dr-9000000000-15c83b0d61366b7e71792021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-thiophenethiol 40V, Positive-QTOFsplash10-0uka-9000000000-6142a21bebf15119f79d2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-thiophenethiol 10V, Negative-QTOFsplash10-004i-0900000000-a37bb8433c512bf79c202021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-thiophenethiol 20V, Negative-QTOFsplash10-004i-5900000000-9f4266ea24977bbe85472021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methyl-3-thiophenethiol 40V, Negative-QTOFsplash10-001i-9000000000-7ccba221be2d45d8a9cd2021-09-22Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-04FELIX labView Spectrum
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
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB019438
KNApSAcK IDNot Available
Chemspider ID30777369
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound55295495
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1880311
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.. .