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Showing metabocard for 3-(Methylthio)thiophene (HMDB0032939)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:52:47 UTC
Update Date2023-02-21 17:22:50 UTC
HMDB IDHMDB0032939
Secondary Accession Numbers
  • HMDB32939
Metabolite Identification
Common Name3-(Methylthio)thiophene
Description3-(Methylthio)thiophene belongs to the class of organic compounds known as aryl thioethers. These are organosulfur compounds containing a thioether group that is substituted by an aryl group. Based on a literature review a significant number of articles have been published on 3-(Methylthio)thiophene.
Structure
Data?1677000170
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0032939 (3-(Methylthio)thiophene)


  Mrv0541 05061306482D          

  7  7  0  0  0  0            999 V2000
    1.2822    2.3518    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
    0.5678    1.9393    0.0000 S   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  2  1  0  0  0  0
  5  4  2  0  0  0  0
  6  1  1  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 HMDB0032939 (3-(Methylthio)thiophene)

HMDB0032939
     RDKit          3D
3-(Methylthio)thiophene
 13 13  0  0  0  0  0  0  0  0999 V2000
    2.4665    0.0349   -0.0255 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1900   -0.7888   -1.0267 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4330   -0.4208   -0.2750 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1808    0.6525   -0.6163 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3786    0.8050    0.0291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4222   -0.5366    1.0774 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9332   -1.2554    0.6778 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7857    0.9987   -0.4830 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3475   -0.6248    0.0776 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0313    0.2994    0.9683 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8660    1.4002   -1.3852 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1244    1.6121   -0.1109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4830   -2.1764    1.0923 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  3  2  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  4 11  1  0
  5 12  1  0
  7 13  1  0
M  END
Download

3D SDF for HMDB0032939 (3-(Methylthio)thiophene)


  Mrv0541 05061306482D          

  7  7  0  0  0  0            999 V2000
    1.2822    2.3518    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
    0.5678    1.9393    0.0000 S   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  2  1  0  0  0  0
  5  4  2  0  0  0  0
  6  1  1  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>
HMDB0032939

> <DATABASE_NAME>
hmdb

> <SMILES>
CSC1=CSC=C1

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

> <INCHI_KEY>
OTYBVBDWIKXFDO-UHFFFAOYSA-N

> <FORMULA>
C5H6S2

> <MOLECULAR_WEIGHT>
130.231

> <EXACT_MASS>
129.991091572

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
13.579236587460585

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-(methylsulfanyl)thiophene

> <ALOGPS_LOGP>
2.52

> <JCHEM_LOGP>
2.3819049073333334

> <ALOGPS_LOGS>
-2.48

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.91591788263886

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
35.9227

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.30e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-(methylsulfanyl)thiophene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0032939 (3-(Methylthio)thiophene)

HMDB0032939
     RDKit          3D
3-(Methylthio)thiophene
 13 13  0  0  0  0  0  0  0  0999 V2000
    2.4665    0.0349   -0.0255 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1900   -0.7888   -1.0267 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4330   -0.4208   -0.2750 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1808    0.6525   -0.6163 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3786    0.8050    0.0291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4222   -0.5366    1.0774 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9332   -1.2554    0.6778 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7857    0.9987   -0.4830 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3475   -0.6248    0.0776 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0313    0.2994    0.9683 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8660    1.4002   -1.3852 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1244    1.6121   -0.1109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4830   -2.1764    1.0923 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  3  2  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  4 11  1  0
  5 12  1  0
  7 13  1  0
M  END
Download

PDB for HMDB0032939 (3-(Methylthio)thiophene)

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       2.393   4.390   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       1.060   3.620   0.000  0.00  0.00           S+0
HETATM    7  S   UNK     0       1.830  -0.290   0.000  0.00  0.00           S+0
CONECT    1    6                                                            
CONECT    2    3    5                                                       
CONECT    3    2    7                                                       
CONECT    4    5    7                                                       
CONECT    5    2    4    6                                                  
CONECT    6    1    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 HMDB0032939 (3-(Methylthio)thiophene)

COMPND    HMDB0032939
HETATM    1  C1  UNL     1       2.467   0.035  -0.026  1.00  0.00           C  
HETATM    2  S1  UNL     1       1.190  -0.789  -1.027  1.00  0.00           S  
HETATM    3  C2  UNL     1      -0.433  -0.421  -0.275  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.181   0.653  -0.616  1.00  0.00           C  
HETATM    5  C4  UNL     1      -2.379   0.805   0.029  1.00  0.00           C  
HETATM    6  S2  UNL     1      -2.422  -0.537   1.077  1.00  0.00           S  
HETATM    7  C5  UNL     1      -0.933  -1.255   0.678  1.00  0.00           C  
HETATM    8  H1  UNL     1       2.786   0.999  -0.483  1.00  0.00           H  
HETATM    9  H2  UNL     1       3.347  -0.625   0.078  1.00  0.00           H  
HETATM   10  H3  UNL     1       2.031   0.299   0.968  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.866   1.400  -1.385  1.00  0.00           H  
HETATM   12  H5  UNL     1      -3.124   1.612  -0.111  1.00  0.00           H  
HETATM   13  H6  UNL     1      -0.483  -2.176   1.092  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3
CONECT    3    4    7    7
CONECT    4    5    5   11
CONECT    5    6   12
CONECT    6    7
CONECT    7   13
END
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SMILES for HMDB0032939 (3-(Methylthio)thiophene)

CSC1=CSC=C1
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INCHI for HMDB0032939 (3-(Methylthio)thiophene)

InChI=1S/C5H6S2/c1-6-5-2-3-7-4-5/h2-4H,1H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
3-(Methylsulfanyl)thiopheneHMDB
3-(methylthio)-ThiopheneHMDB
3-(methylthio)Thiophene, 9ciHMDB
3-ThienylmethylsulfideHMDB
Methyl 3-thienyl sulfideHMDB
Methyl-3-thienylsulfideHMDB
3-(Methylsulphanyl)thiopheneGenerator
Chemical FormulaC5H6S2
Average Molecular Weight130.231
Monoisotopic Molecular Weight129.991091572
IUPAC Name3-(methylsulfanyl)thiophene
Traditional Name3-(methylsulfanyl)thiophene
CAS Registry Number20731-74-2
SMILES
CSC1=CSC=C1
InChI Identifier
InChI=1S/C5H6S2/c1-6-5-2-3-7-4-5/h2-4H,1H3
InChI KeyOTYBVBDWIKXFDO-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as aryl thioethers. These are organosulfur compounds containing a thioether group that is substituted by an aryl group.
KingdomOrganic compounds
Super ClassOrganosulfur compounds
ClassThioethers
Sub ClassAryl thioethers
Direct ParentAryl thioethers
Alternative Parents
Substituents
  • Aryl thioether
  • Alkylarylthioether
  • Heteroaromatic compound
  • Thiophene
  • Organoheterocyclic compound
  • Sulfenyl compound
  • 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 PointNot AvailableNot Available
Water Solubility796.4 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.43 g/LALOGPS
logP2.52ALOGPS
logP2.38ChemAxon
logS-2.5ALOGPS
pKa (Strongest Basic)-7.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity35.92 m³·mol⁻¹ChemAxon
Polarizability13.58 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]+122.4731661259
DarkChem[M-H]-118.19331661259
DeepCCS[M+H]+124.96830932474
DeepCCS[M-H]-122.43230932474
DeepCCS[M-2H]-158.52930932474
DeepCCS[M+Na]+133.08230932474
AllCCS[M+H]+122.032859911
AllCCS[M+H-H2O]+117.232859911
AllCCS[M+NH4]+126.432859911
AllCCS[M+Na]+127.732859911
AllCCS[M-H]-126.632859911
AllCCS[M+Na-2H]-129.632859911
AllCCS[M+HCOO]-132.932859911

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, 2022.3.7 minutes32390414
Predicted by Siyang on May 30, 202214.764 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20220.71 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1614.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid600.3 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid232.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid427.4 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid284.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid565.0 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 Acid578.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)559.2 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1183.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid377.5 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1218.9 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid437.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid429.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate691.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA596.3 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water160.9 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-(Methylthio)thiopheneCSC1=CSC=C11622.3Standard polar33892256
3-(Methylthio)thiopheneCSC1=CSC=C11062.1Standard non polar33892256
3-(Methylthio)thiopheneCSC1=CSC=C11091.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-(Methylthio)thiophene GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-5900000000-57986acfdc283408a9992016-09-22Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-(Methylthio)thiophene 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-(Methylthio)thiophene 10V, Positive-QTOFsplash10-001i-0900000000-f25df04f0c2d4b81f1292016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-(Methylthio)thiophene 20V, Positive-QTOFsplash10-001i-0900000000-b61f34926d0bb5a7e85b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-(Methylthio)thiophene 40V, Positive-QTOFsplash10-0019-9400000000-03dbd29cbc0ec01834762016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-(Methylthio)thiophene 10V, Negative-QTOFsplash10-004i-6900000000-3be97930d074bb343e112016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-(Methylthio)thiophene 20V, Negative-QTOFsplash10-003r-9600000000-89d5d96f5ab0138607a42016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-(Methylthio)thiophene 40V, Negative-QTOFsplash10-0a4l-9000000000-f2a8257152ca532906bb2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-(Methylthio)thiophene 10V, Negative-QTOFsplash10-004i-5900000000-013ca1cd2846aa61417d2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-(Methylthio)thiophene 20V, Negative-QTOFsplash10-001i-9100000000-0611150916f0f8f4c4b12021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-(Methylthio)thiophene 40V, Negative-QTOFsplash10-053r-9000000000-bd7e4c2a1ddcfadda5832021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-(Methylthio)thiophene 10V, Positive-QTOFsplash10-001i-1900000000-243ab9f09151c012853f2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-(Methylthio)thiophene 20V, Positive-QTOFsplash10-001i-8900000000-a54f28b60504a05881232021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-(Methylthio)thiophene 40V, Positive-QTOFsplash10-000i-9000000000-286dadb48a9689feb98c2021-09-22Wishart 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+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 IDFDB010924
KNApSAcK IDNot Available
Chemspider ID453416
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound519806
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1832541
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.. .