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Showing metabocard for 2,3-Dihydro-5-methylthiophene (HMDB0033565)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 18:18:02 UTC
Update Date2023-02-21 17:23:26 UTC
HMDB IDHMDB0033565
Secondary Accession Numbers
  • HMDB33565
Metabolite Identification
Common Name2,3-Dihydro-5-methylthiophene
Description2,3-Dihydro-5-methylthiophene belongs to the class of organic compounds known as dihydrothiophenes. Dihydrothiophenes are compounds containing a dihydrothiophene moiety, which is a thiophene derivative with only one double bond. Based on a literature review a significant number of articles have been published on 2,3-Dihydro-5-methylthiophene.
Structure
Data?1677000206
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0033565 (2,3-Dihydro-5-methylthiophene)


  Mrv0541 05061307112D          

  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
    0.9803   -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    1.1143    0.0000 C   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
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  5  3  2  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
M  END
Download

3D MOL for HMDB0033565 (2,3-Dihydro-5-methylthiophene)

HMDB0033565
     RDKit          3D
2,3-Dihydro-5-methylthiophene
 14 14  0  0  0  0  0  0  0  0999 V2000
   -2.2616    0.4730   -0.4910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8494    0.1194   -0.2589 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2312    0.8040   -0.5213 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5108    0.2196   -0.1882 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4436   -1.2624   -0.0558 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3174   -1.4279    0.4661 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4365    1.5745   -0.5017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9028   -0.0389    0.2606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5468    0.0261   -1.4852 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1503    1.8049   -0.9876 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0277    0.7071    0.6758 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2174    0.4190   -1.0513 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6087   -1.8064   -1.0035 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1248   -1.6121    0.7171 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  1  0
  6  2  1  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
M  END
Download

3D SDF for HMDB0033565 (2,3-Dihydro-5-methylthiophene)


  Mrv0541 05061307112D          

  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
    0.9803   -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    1.1143    0.0000 C   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
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  5  3  2  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0033565

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CCCS1

> <INCHI_IDENTIFIER>
InChI=1S/C5H8S/c1-5-3-2-4-6-5/h3H,2,4H2,1H3

> <INCHI_KEY>
KBUVXRDFMQNIPD-UHFFFAOYSA-N

> <FORMULA>
C5H8S

> <MOLECULAR_WEIGHT>
100.182

> <EXACT_MASS>
100.034670946

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
11.331226240479944

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-methyl-2,3-dihydrothiophene

> <ALOGPS_LOGP>
2.17

> <JCHEM_LOGP>
1.2985835326666664

> <ALOGPS_LOGS>
-0.96

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
32.5417

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.09e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-methyl-4,5-dihydrothiophene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0033565 (2,3-Dihydro-5-methylthiophene)

HMDB0033565
     RDKit          3D
2,3-Dihydro-5-methylthiophene
 14 14  0  0  0  0  0  0  0  0999 V2000
   -2.2616    0.4730   -0.4910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8494    0.1194   -0.2589 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2312    0.8040   -0.5213 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5108    0.2196   -0.1882 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4436   -1.2624   -0.0558 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3174   -1.4279    0.4661 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4365    1.5745   -0.5017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9028   -0.0389    0.2606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5468    0.0261   -1.4852 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1503    1.8049   -0.9876 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0277    0.7071    0.6758 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2174    0.4190   -1.0513 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6087   -1.8064   -1.0035 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1248   -1.6121    0.7171 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  1  0
  6  2  1  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
M  END
Download

PDB for HMDB0033565 (2,3-Dihydro-5-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       1.830  -0.290   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  S   UNK     0      -0.186   1.175   0.000  0.00  0.00           S+0
CONECT    1    5                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2    6                                                       
CONECT    5    1    3    6                                                  
CONECT    6    4    5                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0033565 (2,3-Dihydro-5-methylthiophene)

COMPND    HMDB0033565
HETATM    1  C1  UNL     1      -2.262   0.473  -0.491  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.849   0.119  -0.259  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.231   0.804  -0.521  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.511   0.220  -0.188  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.444  -1.262  -0.056  1.00  0.00           C  
HETATM    6  S1  UNL     1      -0.317  -1.428   0.466  1.00  0.00           S  
HETATM    7  H1  UNL     1      -2.436   1.575  -0.502  1.00  0.00           H  
HETATM    8  H2  UNL     1      -2.903  -0.039   0.261  1.00  0.00           H  
HETATM    9  H3  UNL     1      -2.547   0.026  -1.485  1.00  0.00           H  
HETATM   10  H4  UNL     1       0.150   1.805  -0.988  1.00  0.00           H  
HETATM   11  H5  UNL     1       2.028   0.707   0.676  1.00  0.00           H  
HETATM   12  H6  UNL     1       2.217   0.419  -1.051  1.00  0.00           H  
HETATM   13  H7  UNL     1       1.609  -1.806  -1.004  1.00  0.00           H  
HETATM   14  H8  UNL     1       2.125  -1.612   0.717  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3    3    6
CONECT    3    4   10
CONECT    4    5   11   12
CONECT    5    6   13   14
END
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SMILES for HMDB0033565 (2,3-Dihydro-5-methylthiophene)

CC1=CCCS1
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INCHI for HMDB0033565 (2,3-Dihydro-5-methylthiophene)

InChI=1S/C5H8S/c1-5-3-2-4-6-5/h3H,2,4H2,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2,3-dihydro-5-Methyl-thiopheneHMDB
2-Methyl-4,5-dihydrothiopheneHMDB
5-Methyl-2,3-dihydrothiopheneHMDB
Chemical FormulaC5H8S
Average Molecular Weight100.182
Monoisotopic Molecular Weight100.034670946
IUPAC Name5-methyl-2,3-dihydrothiophene
Traditional Name2-methyl-4,5-dihydrothiophene
CAS Registry Number4610-02-0
SMILES
CC1=CCCS1
InChI Identifier
InChI=1S/C5H8S/c1-5-3-2-4-6-5/h3H,2,4H2,1H3
InChI KeyKBUVXRDFMQNIPD-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dihydrothiophenes. Dihydrothiophenes are compounds containing a dihydrothiophene moiety, which is a thiophene derivative with only one double bond.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDihydrothiophenes
Sub ClassNot Available
Direct ParentDihydrothiophenes
Alternative Parents
Substituents
  • 2,3-dihydrothiophene
  • Thioenolether
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic 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 PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility990.7 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility10.9 g/LALOGPS
logP2.17ALOGPS
logP1.3ChemAxon
logS-0.96ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity32.54 m³·mol⁻¹ChemAxon
Polarizability11.33 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]+119.99931661259
DarkChem[M-H]-114.17631661259
DeepCCS[M+H]+124.53730932474
DeepCCS[M-H]-122.61830932474
DeepCCS[M-2H]-158.11730932474
DeepCCS[M+Na]+132.5630932474
AllCCS[M+H]+115.932859911
AllCCS[M+H-H2O]+110.832859911
AllCCS[M+NH4]+120.632859911
AllCCS[M+Na]+122.032859911
AllCCS[M-H]-127.032859911
AllCCS[M+Na-2H]-130.732859911
AllCCS[M+HCOO]-134.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2,3-Dihydro-5-methylthiopheneCC1=CCCS11177.2Standard polar33892256
2,3-Dihydro-5-methylthiopheneCC1=CCCS1859.0Standard non polar33892256
2,3-Dihydro-5-methylthiopheneCC1=CCCS1860.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2,3-Dihydro-5-methylthiophene GC-MS (Non-derivatized) - 70eV, Positivesplash10-0umu-9200000000-9aff929da0ca0d21e4942017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2,3-Dihydro-5-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 - 2,3-Dihydro-5-methylthiophene 10V, Positive-QTOFsplash10-0udi-0900000000-4a61920ceb770dd5f8232016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydro-5-methylthiophene 20V, Positive-QTOFsplash10-0udi-4900000000-9d545167052b29f39cdf2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydro-5-methylthiophene 40V, Positive-QTOFsplash10-0f79-9100000000-80d2ab35a8adb87e289f2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydro-5-methylthiophene 10V, Negative-QTOFsplash10-006t-9000000000-5e301efe7f16a142bf1b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydro-5-methylthiophene 20V, Negative-QTOFsplash10-0002-9000000000-d243168649c189dccf162016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydro-5-methylthiophene 40V, Negative-QTOFsplash10-053r-9000000000-45c879067ee523de2f9e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydro-5-methylthiophene 10V, Negative-QTOFsplash10-0002-9000000000-daf914b686710e8c17fe2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydro-5-methylthiophene 20V, Negative-QTOFsplash10-00ls-9000000000-eba8263055cc38cd48ff2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydro-5-methylthiophene 40V, Negative-QTOFsplash10-001i-9000000000-4a211d05504089ea0ae32021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydro-5-methylthiophene 10V, Positive-QTOFsplash10-0udi-1900000000-931fe900d0a093cd18d32021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydro-5-methylthiophene 20V, Positive-QTOFsplash10-0fk9-9300000000-1a3e932f71fc692974882021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dihydro-5-methylthiophene 40V, Positive-QTOFsplash10-0a4i-9000000000-fd3dd253387a9e3952712021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 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, 1000 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C 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 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 IDFDB011635
KNApSAcK IDC00055627
Chemspider ID486016
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound559083
PDB IDNot Available
ChEBI ID167067
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1836721
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.. .