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Showing metabocard for 3-Methyl-2-cyclopentene-1-thione (HMDB0302175)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 15:16:07 UTC
Update Date2021-09-23 15:16:07 UTC
HMDB IDHMDB0302175
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-Methyl-2-cyclopentene-1-thione
Description3-methyl-2-cyclopentene-1-thione is a member of the class of compounds known as thioketones. Thioketones are compounds in which the oxygen of a ketone has been replaced by divalent sulfur R2C=S ( R not H ). Thioketones that have an alpha-hydrogen interconvert with Thioenols. Moreover, they interconvert with thioaldehydes. 3-methyl-2-cyclopentene-1-thione is slightly soluble (in water) and an extremely weak acidic compound (based on its pKa). 3-methyl-2-cyclopentene-1-thione can be found in soft-necked garlic, which makes 3-methyl-2-cyclopentene-1-thione a potential biomarker for the consumption of this food product.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302175 (3-Methyl-2-cyclopentene-1-thione)


  Mrv1533007131513272D          

  7  7  0  0  0  0            999 V2000
   -0.3297   -0.8227    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
   -0.0997    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
    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
  3  2  1  0  0  0  0
  5  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  4  2  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  6  2  0  0  0  0
M  END
Download

3D MOL for HMDB0302175 (3-Methyl-2-cyclopentene-1-thione)

HMDB0302175
     RDKit          3D
3-Methyl-2-cyclopentene-1-thione
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.0889    0.2549   -0.3324 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6177    0.2104   -0.1311 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1947    1.2344    0.0605 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5704    0.7780    0.2171 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9218    1.6688    0.1969 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5357   -0.6910    0.4055 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1824   -1.0343   -0.1166 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5367   -0.7455   -0.1340 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2720    0.4732   -1.4016 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5957    0.9719    0.3163 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1566    2.2778    0.0915 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6369   -0.8857    1.5072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3087   -1.2072   -0.1825 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2851   -1.7655    0.6056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2019   -1.5403   -1.1024 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  2  0
  4  6  1  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
  6 12  1  0
  6 13  1  0
  7 14  1  0
  7 15  1  0
M  END
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3D SDF for HMDB0302175 (3-Methyl-2-cyclopentene-1-thione)


  Mrv1533007131513272D          

  7  7  0  0  0  0            999 V2000
   -0.3297   -0.8227    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
   -0.0997    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
    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
  3  2  1  0  0  0  0
  5  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  4  2  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  6  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302175

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H8S/c1-5-2-3-6(7)4-5/h4H,2-3H2,1H3

> <INCHI_KEY>
JBWUENDATZQNBX-UHFFFAOYSA-N

> <FORMULA>
C6H8S

> <MOLECULAR_WEIGHT>
112.19

> <EXACT_MASS>
112.034671432

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
12.91356913273319

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methylcyclopent-2-ene-1-thione

> <ALOGPS_LOGP>
1.16

> <JCHEM_LOGP>
2.174679945333333

> <ALOGPS_LOGS>
-1.72

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
19.143685108817056

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
37.0126

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.15e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-methylcyclopent-2-ene-1-thione

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0302175 (3-Methyl-2-cyclopentene-1-thione)

HMDB0302175
     RDKit          3D
3-Methyl-2-cyclopentene-1-thione
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.0889    0.2549   -0.3324 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6177    0.2104   -0.1311 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1947    1.2344    0.0605 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5704    0.7780    0.2171 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9218    1.6688    0.1969 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5357   -0.6910    0.4055 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1824   -1.0343   -0.1166 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5367   -0.7455   -0.1340 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2720    0.4732   -1.4016 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5957    0.9719    0.3163 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1566    2.2778    0.0915 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6369   -0.8857    1.5072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3087   -1.2072   -0.1825 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2851   -1.7655    0.6056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2019   -1.5403   -1.1024 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  2  0
  4  6  1  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
  6 12  1  0
  6 13  1  0
  7 14  1  0
  7 15  1  0
M  END
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PDB for HMDB0302175 (3-Methyl-2-cyclopentene-1-thione)

HEADER    PROTEIN                                 13-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUL-15         0                                  
HETATM    1  C   UNK     0      -0.615  -1.536   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      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    7  S   UNK     0       1.060   3.620   0.000  0.00  0.00           S+0
CONECT    1    5                                                            
CONECT    2    3    5                                                       
CONECT    3    2    6                                                       
CONECT    4    5    6                                                       
CONECT    5    1    2    4                                                  
CONECT    6    3    4    7                                                  
CONECT    7    6                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0302175 (3-Methyl-2-cyclopentene-1-thione)

COMPND    HMDB0302175
HETATM    1  C1  UNL     1       2.089   0.255  -0.332  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.618   0.210  -0.131  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.195   1.234   0.060  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.570   0.778   0.217  1.00  0.00           C  
HETATM    5  S1  UNL     1      -2.922   1.669   0.197  1.00  0.00           S  
HETATM    6  C5  UNL     1      -1.536  -0.691   0.406  1.00  0.00           C  
HETATM    7  C6  UNL     1      -0.182  -1.034  -0.117  1.00  0.00           C  
HETATM    8  H1  UNL     1       2.537  -0.745  -0.134  1.00  0.00           H  
HETATM    9  H2  UNL     1       2.272   0.473  -1.402  1.00  0.00           H  
HETATM   10  H3  UNL     1       2.596   0.972   0.316  1.00  0.00           H  
HETATM   11  H4  UNL     1       0.157   2.278   0.091  1.00  0.00           H  
HETATM   12  H5  UNL     1      -1.637  -0.886   1.507  1.00  0.00           H  
HETATM   13  H6  UNL     1      -2.309  -1.207  -0.182  1.00  0.00           H  
HETATM   14  H7  UNL     1       0.285  -1.765   0.606  1.00  0.00           H  
HETATM   15  H8  UNL     1      -0.202  -1.540  -1.102  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    3    7
CONECT    3    4   11
CONECT    4    5    5    6
CONECT    6    7   12   13
CONECT    7   14   15
END
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SMILES for HMDB0302175 (3-Methyl-2-cyclopentene-1-thione)

CC1=CC(=S)CC1
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INCHI for HMDB0302175 (3-Methyl-2-cyclopentene-1-thione)

InChI=1S/C6H8S/c1-5-2-3-6(7)4-5/h4H,2-3H2,1H3
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC6H8S
Average Molecular Weight112.19
Monoisotopic Molecular Weight112.034671432
IUPAC Name3-methylcyclopent-2-ene-1-thione
Traditional Name3-methylcyclopent-2-ene-1-thione
CAS Registry NumberNot Available
SMILES
CC1=CC(=S)CC1
InChI Identifier
InChI=1S/C6H8S/c1-5-2-3-6(7)4-5/h4H,2-3H2,1H3
InChI KeyJBWUENDATZQNBX-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as thioketones. Thioketones are compounds in which the oxygen of a ketone has been replaced by divalent sulfur R2C=S ( R not H ). Thioketones that have an alpha-hydrogen interconvert with Thioenols. Moreover, they interconvert with thioaldehydes.
KingdomOrganic compounds
Super ClassOrganosulfur compounds
ClassThiocarbonyl compounds
Sub ClassThioketones
Direct ParentThioketones
Alternative Parents
Substituents
  • Thioketone
  • Hydrocarbon derivative
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP1.16ALOGPS
logP2.17ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)19.14ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity37.01 m³·mol⁻¹ChemAxon
Polarizability12.91 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
AllCCS[M+H]+121.3632859911
AllCCS[M+H-H2O]+116.50232859911
AllCCS[M+Na]+127.20732859911
AllCCS[M+NH4]+125.89732859911
AllCCS[M-H]-123.30132859911
AllCCS[M+Na-2H]-126.47832859911
AllCCS[M+HCOO]-129.99732859911
DeepCCS[M+H]+126.13330932474
DeepCCS[M-H]-123.16330932474
DeepCCS[M-2H]-159.6230932474
DeepCCS[M+Na]+134.69730932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyl-2-cyclopentene-1-thione 10V, Positive-QTOFsplash10-03di-3900000000-7e501c229603305d5a412016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyl-2-cyclopentene-1-thione 20V, Positive-QTOFsplash10-03di-9800000000-796715eb51a49a6fbf112016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyl-2-cyclopentene-1-thione 40V, Positive-QTOFsplash10-0udi-9000000000-c4a68470267818334ac02016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyl-2-cyclopentene-1-thione 10V, Negative-QTOFsplash10-03di-3900000000-f8f4b67f412982935db12016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyl-2-cyclopentene-1-thione 20V, Negative-QTOFsplash10-03di-4900000000-edf821efd86010a76ae62016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyl-2-cyclopentene-1-thione 40V, Negative-QTOFsplash10-08gl-9200000000-6fc86d5f3a2b02f1017a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyl-2-cyclopentene-1-thione 10V, Positive-QTOFsplash10-03di-2900000000-ef48d52c26d6c1a92fd12021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyl-2-cyclopentene-1-thione 20V, Positive-QTOFsplash10-03di-9500000000-a3d26a19a6d011e5618e2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyl-2-cyclopentene-1-thione 40V, Positive-QTOFsplash10-0570-9000000000-4fc0067e2255791421182021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyl-2-cyclopentene-1-thione 10V, Negative-QTOFsplash10-03di-0900000000-0b420ab7e14ab10017dc2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyl-2-cyclopentene-1-thione 20V, Negative-QTOFsplash10-03di-4900000000-f490303cbafdc8a20ba42021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyl-2-cyclopentene-1-thione 40V, Negative-QTOFsplash10-06si-9300000000-2d47cc4f8c2608f9d0712021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
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 IDFDB003547
KNApSAcK IDNot Available
Chemspider ID23253950
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound14252428
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available