Hmdb loader

Showing metabocard for 2-Thiophenemethanethiol (HMDB0031853)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:45:58 UTC
Update Date2023-02-21 17:21:23 UTC
HMDB IDHMDB0031853
Secondary Accession Numbers
  • HMDB31853
Metabolite Identification
Common Name2-Thiophenemethanethiol
Description2-Thiophenemethanethiol 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. 2-Thiophenemethanethiol is a coffee, fishy, and roast tasting compound. Based on a literature review a significant number of articles have been published on 2-Thiophenemethanethiol.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031853 (2-Thiophenemethanethiol)


  Mrv0541 05061306102D          

  7  7  0  0  0  0            999 V2000
    0.9803   -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
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    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
   -0.1467    2.3518    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
  2  1  1  0  0  0  0
  3  1  2  0  0  0  0
  5  2  2  0  0  0  0
  5  4  1  0  0  0  0
  6  4  1  0  0  0  0
  7  3  1  0  0  0  0
  7  5  1  0  0  0  0
M  END
Download

3D MOL for HMDB0031853 (2-Thiophenemethanethiol)

HMDB0031853
     RDKit          3D
2-Thiophenemethanethiol
 13 13  0  0  0  0  0  0  0  0999 V2000
   -2.8542    0.2667    0.2555 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6791   -0.8894   -0.4410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2952   -0.4431   -0.0968 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5399    0.3908   -0.7930 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7429    0.6354   -0.2643 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0466    0.0364    0.9274 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6332   -0.8561    1.2751 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2039    1.4866    0.5266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8004   -1.9332   -0.0742 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7725   -0.9403   -1.5551 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1671    0.8112   -1.7515 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4835    1.2980   -0.7587 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9922    0.1370    1.4898 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  2  0
  6  7  1  0
  7  3  1  0
  1  8  1  0
  2  9  1  0
  2 10  1  0
  4 11  1  0
  5 12  1  0
  6 13  1  0
M  END
Download

3D SDF for HMDB0031853 (2-Thiophenemethanethiol)


  Mrv0541 05061306102D          

  7  7  0  0  0  0            999 V2000
    0.9803   -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
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    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
   -0.1467    2.3518    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
  2  1  1  0  0  0  0
  3  1  2  0  0  0  0
  5  2  2  0  0  0  0
  5  4  1  0  0  0  0
  6  4  1  0  0  0  0
  7  3  1  0  0  0  0
  7  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0031853

> <DATABASE_NAME>
hmdb

> <SMILES>
SCC1=CC=CS1

> <INCHI_IDENTIFIER>
InChI=1S/C5H6S2/c6-4-5-2-1-3-7-5/h1-3,6H,4H2

> <INCHI_KEY>
GCZQHDFWKVMZOE-UHFFFAOYSA-N

> <FORMULA>
C5H6S2

> <MOLECULAR_WEIGHT>
130.231

> <EXACT_MASS>
129.991091572

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
13.551423562169312

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
thiophen-2-ylmethanethiol

> <ALOGPS_LOGP>
2.73

> <JCHEM_LOGP>
2.3701468176666665

> <ALOGPS_LOGS>
-2.86

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.83847780471758

> <JCHEM_PKA_STRONGEST_BASIC>
-8.104844500109628

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
35.9464

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.79e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thiophen-2-ylmethanethiol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0031853 (2-Thiophenemethanethiol)

HMDB0031853
     RDKit          3D
2-Thiophenemethanethiol
 13 13  0  0  0  0  0  0  0  0999 V2000
   -2.8542    0.2667    0.2555 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6791   -0.8894   -0.4410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2952   -0.4431   -0.0968 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5399    0.3908   -0.7930 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7429    0.6354   -0.2643 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0466    0.0364    0.9274 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6332   -0.8561    1.2751 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2039    1.4866    0.5266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8004   -1.9332   -0.0742 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7725   -0.9403   -1.5551 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1671    0.8112   -1.7515 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4835    1.2980   -0.7587 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9922    0.1370    1.4898 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  2  0
  6  7  1  0
  7  3  1  0
  1  8  1  0
  2  9  1  0
  2 10  1  0
  4 11  1  0
  5 12  1  0
  6 13  1  0
M  END
Download

PDB for HMDB0031853 (2-Thiophenemethanethiol)

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       1.830  -0.290   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   3.620   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      -0.274   4.390   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    2    3                                                       
CONECT    2    1    5                                                       
CONECT    3    1    7                                                       
CONECT    4    5    6                                                       
CONECT    5    2    4    7                                                  
CONECT    6    4                                                            
CONECT    7    3    5                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
Download

3D PDB for HMDB0031853 (2-Thiophenemethanethiol)

COMPND    HMDB0031853
HETATM    1  S1  UNL     1      -2.854   0.267   0.255  1.00  0.00           S  
HETATM    2  C1  UNL     1      -1.679  -0.889  -0.441  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.295  -0.443  -0.097  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.540   0.391  -0.793  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.743   0.635  -0.264  1.00  0.00           C  
HETATM    6  C5  UNL     1       2.047   0.036   0.927  1.00  0.00           C  
HETATM    7  S2  UNL     1       0.633  -0.856   1.275  1.00  0.00           S  
HETATM    8  H1  UNL     1      -2.204   1.487   0.527  1.00  0.00           H  
HETATM    9  H2  UNL     1      -1.800  -1.933  -0.074  1.00  0.00           H  
HETATM   10  H3  UNL     1      -1.773  -0.940  -1.555  1.00  0.00           H  
HETATM   11  H4  UNL     1       0.167   0.811  -1.752  1.00  0.00           H  
HETATM   12  H5  UNL     1       2.484   1.298  -0.759  1.00  0.00           H  
HETATM   13  H6  UNL     1       2.992   0.137   1.490  1.00  0.00           H  
CONECT    1    2    8
CONECT    2    3    9   10
CONECT    3    4    4    7
CONECT    4    5   11
CONECT    5    6    6   12
CONECT    6    7   13
END
Download

SMILES for HMDB0031853 (2-Thiophenemethanethiol)

SCC1=CC=CS1
Download

INCHI for HMDB0031853 (2-Thiophenemethanethiol)

InChI=1S/C5H6S2/c6-4-5-2-1-3-7-5/h1-3,6H,4H2
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
2-(Mercaptomethyl)thiopheneHMDB
2-Thenyl mercaptanHMDB
2-ThenylmercaptanHMDB
2-ThenylthiolHMDB
2-ThienylmethanethiolHMDB
2-ThiophenemethenethiolHMDB
Thenyl mercaptanHMDB
Thiophene-2-methanethiolHMDB
Chemical FormulaC5H6S2
Average Molecular Weight130.231
Monoisotopic Molecular Weight129.991091572
IUPAC Namethiophen-2-ylmethanethiol
Traditional Namethiophen-2-ylmethanethiol
CAS Registry Number6258-63-5
SMILES
SCC1=CC=CS1
InChI Identifier
InChI=1S/C5H6S2/c6-4-5-2-1-3-7-5/h1-3,6H,4H2
InChI KeyGCZQHDFWKVMZOE-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
  • Alkylthiol
  • Hydrocarbon derivative
  • Organosulfur compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationSource
ProcessNot Available
Role
Industrial application
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point166.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility0The Good Scents Company Information System
LogP2.334 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.18 g/LALOGPS
logP2.73ALOGPS
logP2.37ChemAxon
logS-2.9ALOGPS
pKa (Strongest Acidic)9.84ChemAxon
pKa (Strongest Basic)-8.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity35.95 m³·mol⁻¹ChemAxon
Polarizability13.55 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]+122.89731661259
DarkChem[M-H]-118.55331661259
DeepCCS[M+H]+127.10730932474
DeepCCS[M-H]-125.18630932474
DeepCCS[M-2H]-160.72630932474
DeepCCS[M+Na]+135.16130932474
AllCCS[M+H]+122.932859911
AllCCS[M+H-H2O]+118.132859911
AllCCS[M+NH4]+127.432859911
AllCCS[M+Na]+128.732859911
AllCCS[M-H]-125.932859911
AllCCS[M+Na-2H]-128.932859911
AllCCS[M+HCOO]-132.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-ThiophenemethanethiolSCC1=CC=CS11698.6Standard polar33892256
2-ThiophenemethanethiolSCC1=CC=CS11057.8Standard non polar33892256
2-ThiophenemethanethiolSCC1=CC=CS11090.7Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-Thiophenemethanethiol,1TMS,isomer #1C[Si](C)(C)SCC1=CC=CS11337.6Semi standard non polar33892256
2-Thiophenemethanethiol,1TMS,isomer #1C[Si](C)(C)SCC1=CC=CS11189.7Standard non polar33892256
2-Thiophenemethanethiol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SCC1=CC=CS11562.5Semi standard non polar33892256
2-Thiophenemethanethiol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SCC1=CC=CS11439.0Standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2-Thiophenemethanethiol GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9200000000-1a10fdeef386965883dd2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Thiophenemethanethiol 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 - 2-Thiophenemethanethiol 10V, Positive-QTOFsplash10-001i-0900000000-fd4c5496c910a0bf0d532016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Thiophenemethanethiol 20V, Positive-QTOFsplash10-001i-1900000000-d11642303a2a37cdc48e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Thiophenemethanethiol 40V, Positive-QTOFsplash10-0uej-9000000000-598c6ff4dc6b3727a2a12016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Thiophenemethanethiol 10V, Negative-QTOFsplash10-004i-1900000000-bdb94b5d422ad73a64f32016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Thiophenemethanethiol 20V, Negative-QTOFsplash10-0059-9700000000-ea39e2ed081a2fd6f4752016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Thiophenemethanethiol 40V, Negative-QTOFsplash10-0a4i-9000000000-0459a85c6e605c8c39612016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Thiophenemethanethiol 10V, Negative-QTOFsplash10-0059-4900000000-f2fbae062ced633633d82021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Thiophenemethanethiol 20V, Negative-QTOFsplash10-00ai-9500000000-cf3a0eca90cfaf12341a2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Thiophenemethanethiol 40V, Negative-QTOFsplash10-001i-9000000000-11032f79692cc0fdf57d2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Thiophenemethanethiol 10V, Positive-QTOFsplash10-001j-7900000000-3520dd2bf0771169c0282021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Thiophenemethanethiol 20V, Positive-QTOFsplash10-0002-9000000000-bc6c4c118658f31223122021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Thiophenemethanethiol 40V, Positive-QTOFsplash10-0udj-9000000000-5ef1370f36052cad65952021-09-22Wishart 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 IDFDB008537
KNApSAcK IDNot Available
Chemspider ID72624
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound80408
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1034941
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.. .