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Showing metabocard for Cyclopentanethiol (HMDB0039771)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 01:18:39 UTC
Update Date2023-02-21 17:27:07 UTC
HMDB IDHMDB0039771
Secondary Accession Numbers
  • HMDB39771
Metabolite Identification
Common NameCyclopentanethiol
DescriptionCyclopentanethiol belongs to the class of organic compounds known as alkylthiols. These are organic compounds containing the thiol functional group linked to an alkyl chain. Cyclopentanethiol is an alliaceous, celery, and citrus tasting compound. Based on a literature review very few articles have been published on Cyclopentanethiol.
Structure
Data?1677000427
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0039771 (Cyclopentanethiol)


  Mrv0541 05061311232D          

  6  6  0  0  0  0            999 V2000
    0.1553   -0.1553    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
   -0.0997    0.6294    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
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
M  END
Download

3D MOL for HMDB0039771 (Cyclopentanethiol)

HMDB0039771
     RDKit          3D
Cyclopentanethiol
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.6042    0.3075    0.2409 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.9281    0.1976   -0.4411 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2754   -1.1186   -0.1786 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0361   -0.8729    0.4997 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3233    0.5789    0.0942 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0513    1.1756    0.3073 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6191    0.2625    1.6367 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9893    0.4750   -1.5061 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8765   -1.7760    0.5062 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0943   -1.6847   -1.1038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8422   -1.5489    0.1951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9311   -0.8522    1.6157 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6543    0.6084   -0.9515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0929    1.0247    0.7449 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1459    2.2060   -0.0227 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2957    1.0170    1.3895 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  1  0
  5  6  1  0
  6  2  1  0
  1  7  1  0
  2  8  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
M  END
Download

3D SDF for HMDB0039771 (Cyclopentanethiol)


  Mrv0541 05061311232D          

  6  6  0  0  0  0            999 V2000
    0.1553   -0.1553    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
   -0.0997    0.6294    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
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0039771

> <DATABASE_NAME>
hmdb

> <SMILES>
SC1CCCC1

> <INCHI_IDENTIFIER>
InChI=1S/C5H10S/c6-5-3-1-2-4-5/h5-6H,1-4H2

> <INCHI_KEY>
WVDYBOADDMMFIY-UHFFFAOYSA-N

> <FORMULA>
C5H10S

> <MOLECULAR_WEIGHT>
102.198

> <EXACT_MASS>
102.05032101

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
12.095318293388695

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
cyclopentanethiol

> <ALOGPS_LOGP>
2.54

> <JCHEM_LOGP>
1.9837162296666664

> <ALOGPS_LOGS>
-2.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.066617455784215

> <JCHEM_PKA_STRONGEST_BASIC>
-9.6751387444479

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
30.7523

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.12e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cyclopentanethiol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0039771 (Cyclopentanethiol)

HMDB0039771
     RDKit          3D
Cyclopentanethiol
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.6042    0.3075    0.2409 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.9281    0.1976   -0.4411 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2754   -1.1186   -0.1786 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0361   -0.8729    0.4997 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3233    0.5789    0.0942 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0513    1.1756    0.3073 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6191    0.2625    1.6367 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9893    0.4750   -1.5061 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8765   -1.7760    0.5062 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0943   -1.6847   -1.1038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8422   -1.5489    0.1951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9311   -0.8522    1.6157 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6543    0.6084   -0.9515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0929    1.0247    0.7449 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1459    2.2060   -0.0227 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2957    1.0170    1.3895 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  1  0
  5  6  1  0
  6  2  1  0
  1  7  1  0
  2  8  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
M  END
Download

PDB for HMDB0039771 (Cyclopentanethiol)

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       0.290  -0.290   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      -0.186   1.175   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
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    5                                                       
CONECT    5    3    4    6                                                  
CONECT    6    5                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0039771 (Cyclopentanethiol)

COMPND    HMDB0039771
HETATM    1  S1  UNL     1       2.604   0.307   0.241  1.00  0.00           S  
HETATM    2  C1  UNL     1       0.928   0.198  -0.441  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.275  -1.119  -0.179  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.036  -0.873   0.500  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.323   0.579   0.094  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.051   1.176   0.307  1.00  0.00           C  
HETATM    7  H1  UNL     1       2.619   0.262   1.637  1.00  0.00           H  
HETATM    8  H2  UNL     1       0.989   0.475  -1.506  1.00  0.00           H  
HETATM    9  H3  UNL     1       0.876  -1.776   0.506  1.00  0.00           H  
HETATM   10  H4  UNL     1       0.094  -1.685  -1.104  1.00  0.00           H  
HETATM   11  H5  UNL     1      -1.842  -1.549   0.195  1.00  0.00           H  
HETATM   12  H6  UNL     1      -0.931  -0.852   1.616  1.00  0.00           H  
HETATM   13  H7  UNL     1      -1.654   0.608  -0.951  1.00  0.00           H  
HETATM   14  H8  UNL     1      -2.093   1.025   0.745  1.00  0.00           H  
HETATM   15  H9  UNL     1       0.146   2.206  -0.023  1.00  0.00           H  
HETATM   16  H10 UNL     1       0.296   1.017   1.389  1.00  0.00           H  
CONECT    1    2    7
CONECT    2    3    6    8
CONECT    3    4    9   10
CONECT    4    5   11   12
CONECT    5    6   13   14
CONECT    6   15   16
END
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SMILES for HMDB0039771 (Cyclopentanethiol)

SC1CCCC1
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INCHI for HMDB0039771 (Cyclopentanethiol)

InChI=1S/C5H10S/c6-5-3-1-2-4-5/h5-6H,1-4H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Cyclopentyl mercaptanHMDB
Cyclopentyl sulfideHMDB
CyclopentylthiolHMDB
FEMA 3262HMDB
MercaptocyclopentaneHMDB
Chemical FormulaC5H10S
Average Molecular Weight102.198
Monoisotopic Molecular Weight102.05032101
IUPAC Namecyclopentanethiol
Traditional Namecyclopentanethiol
CAS Registry Number1679-07-8
SMILES
SC1CCCC1
InChI Identifier
InChI=1S/C5H10S/c6-5-3-1-2-4-5/h5-6H,1-4H2
InChI KeyWVDYBOADDMMFIY-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alkylthiols. These are organic compounds containing the thiol functional group linked to an alkyl chain.
KingdomOrganic compounds
Super ClassOrganosulfur compounds
ClassThiols
Sub ClassAlkylthiols
Direct ParentAlkylthiols
Alternative Parents
Substituents
  • Alkylthiol
  • Hydrocarbon derivative
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationSource
ProcessNot Available
Role
Biological roleIndustrial application
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point41.00 to 42.00 °C. @ 16.00 mm HgThe Good Scents Company Information System
Water Solubility758 mg/L @ 25 °C (calc.)The Good Scents Company Information System
LogP2.377 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.81 g/LALOGPS
logP2.54ALOGPS
logP1.98ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)10.07ChemAxon
pKa (Strongest Basic)-9.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity30.75 m³·mol⁻¹ChemAxon
Polarizability12.1 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]+119.26831661259
DarkChem[M-H]-112.26831661259
DeepCCS[M+H]+126.39730932474
DeepCCS[M-H]-124.46930932474
DeepCCS[M-2H]-159.87930932474
DeepCCS[M+Na]+134.36930932474
AllCCS[M+H]+123.232859911
AllCCS[M+H-H2O]+118.432859911
AllCCS[M+NH4]+127.832859911
AllCCS[M+Na]+129.132859911
AllCCS[M-H]-126.632859911
AllCCS[M+Na-2H]-130.532859911
AllCCS[M+HCOO]-134.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
CyclopentanethiolSC1CCCC11122.4Standard polar33892256
CyclopentanethiolSC1CCCC1841.5Standard non polar33892256
CyclopentanethiolSC1CCCC1832.9Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Cyclopentanethiol,1TMS,isomer #1C[Si](C)(C)SC1CCCC11064.1Semi standard non polar33892256
Cyclopentanethiol,1TMS,isomer #1C[Si](C)(C)SC1CCCC11091.0Standard non polar33892256
Cyclopentanethiol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SC1CCCC11334.9Semi standard non polar33892256
Cyclopentanethiol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SC1CCCC11305.3Standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Cyclopentanethiol GC-MS (Non-derivatized) - 70eV, Positivesplash10-016r-9100000000-f84522f41b31ae86ae032017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cyclopentanethiol 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 - Cyclopentanethiol 10V, Positive-QTOFsplash10-0udi-4900000000-30e249a405770c2581c82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanethiol 20V, Positive-QTOFsplash10-0udi-5900000000-d2a2bdccbb164450f30d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanethiol 40V, Positive-QTOFsplash10-0a4l-9000000000-3133494c4ceb1ae374e02016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanethiol 10V, Negative-QTOFsplash10-0uxr-9800000000-1d44bb4cb3db90b4f5db2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanethiol 20V, Negative-QTOFsplash10-0uxr-7900000000-6b657a15c1a834da12862016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanethiol 40V, Negative-QTOFsplash10-053r-9000000000-ebefb96e422137c61eef2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanethiol 10V, Negative-QTOFsplash10-0udi-0900000000-8a3d491a8e03014f71422021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanethiol 20V, Negative-QTOFsplash10-0uxr-6900000000-c1eae8a8de5278116c532021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanethiol 40V, Negative-QTOFsplash10-001i-9300000000-6b3e3f7014020e1f0c572021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanethiol 10V, Positive-QTOFsplash10-014i-9300000000-edd002726ee71a086d612021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanethiol 20V, Positive-QTOFsplash10-014i-9100000000-e05d4c17314ff1d5404e2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanethiol 40V, Positive-QTOFsplash10-01ox-9000000000-80479cda59d00743e4a22021-09-25Wishart 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+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 IDFDB019419
KNApSAcK IDNot Available
Chemspider ID14757
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound15510
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1015151
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.. .