Hmdb loader
Survey

Showing metabocard for 1-Pentanethiol (HMDB0032457)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:49:54 UTC
Update Date2023-02-21 17:22:11 UTC
HMDB IDHMDB0032457
Secondary Accession Numbers
  • HMDB32457
Metabolite Identification
Common Name1-Pentanethiol
Description1-Pentanethiol, also known as amyl mercaptan or N-pentylmercaptan, belongs to the class of organic compounds known as alkylthiols. These are organic compounds containing the thiol functional group linked to an alkyl chain. Based on a literature review a significant number of articles have been published on 1-Pentanethiol.
Structure
Data?1677000131
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0032457 (1-Pentanethiol)


  Mrv0541 05061306312D          

  6  5  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  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 HMDB0032457 (1-Pentanethiol)

HMDB0032457
     RDKit          3D
1-Pentanethiol
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.5917   -0.3776   -0.1112 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1355   -0.5068   -0.4895 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3926    0.7040   -0.0024 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0644    0.6726   -0.3288 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7891   -0.5015    0.2665 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5398   -0.4289   -0.1975 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0345   -1.3867   -0.0325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1798    0.1923   -0.8701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7327    0.1734    0.8445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7400   -1.4578   -0.1037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0748   -0.5009   -1.6023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8129    1.5789   -0.5781 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6105    0.9240    1.0573 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5123    1.6281    0.0195 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1586    0.6791   -1.4341 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3787   -1.4360   -0.2100 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6664   -0.5983    1.3441 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1957    0.6421    0.4007 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
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  0
M  END
Download

3D SDF for HMDB0032457 (1-Pentanethiol)


  Mrv0541 05061306312D          

  6  5  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0032457

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCS

> <INCHI_IDENTIFIER>
InChI=1S/C5H12S/c1-2-3-4-5-6/h6H,2-5H2,1H3

> <INCHI_KEY>
ZRKMQKLGEQPLNS-UHFFFAOYSA-N

> <FORMULA>
C5H12S

> <MOLECULAR_WEIGHT>
104.214

> <EXACT_MASS>
104.065971074

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
13.320776025973837

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pentane-1-thiol

> <ALOGPS_LOGP>
3.02

> <JCHEM_LOGP>
2.501260007

> <ALOGPS_LOGS>
-2.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.200825439175754

> <JCHEM_PKA_STRONGEST_BASIC>
-9.559569341348979

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
32.7645

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.20e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-pentanethiol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0032457 (1-Pentanethiol)

HMDB0032457
     RDKit          3D
1-Pentanethiol
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.5917   -0.3776   -0.1112 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1355   -0.5068   -0.4895 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3926    0.7040   -0.0024 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0644    0.6726   -0.3288 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7891   -0.5015    0.2665 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5398   -0.4289   -0.1975 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0345   -1.3867   -0.0325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1798    0.1923   -0.8701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7327    0.1734    0.8445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7400   -1.4578   -0.1037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0748   -0.5009   -1.6023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8129    1.5789   -0.5781 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6105    0.9240    1.0573 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5123    1.6281    0.0195 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1586    0.6791   -1.4341 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3787   -1.4360   -0.2100 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6664   -0.5983    1.3441 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1957    0.6421    0.4007 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
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  0
M  END
Download

PDB for HMDB0032457 (1-Pentanethiol)

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      -0.357   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    6  S   UNK     0       6.311   2.104   0.000  0.00  0.00           S+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
Download

3D PDB for HMDB0032457 (1-Pentanethiol)

COMPND    HMDB0032457
HETATM    1  C1  UNL     1      -2.592  -0.378  -0.111  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.136  -0.507  -0.490  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.393   0.704  -0.002  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.064   0.673  -0.329  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.789  -0.502   0.266  1.00  0.00           C  
HETATM    6  S1  UNL     1       3.540  -0.429  -0.197  1.00  0.00           S  
HETATM    7  H1  UNL     1      -3.034  -1.387  -0.033  1.00  0.00           H  
HETATM    8  H2  UNL     1      -3.180   0.192  -0.870  1.00  0.00           H  
HETATM    9  H3  UNL     1      -2.733   0.173   0.845  1.00  0.00           H  
HETATM   10  H4  UNL     1      -0.740  -1.458  -0.104  1.00  0.00           H  
HETATM   11  H5  UNL     1      -1.075  -0.501  -1.602  1.00  0.00           H  
HETATM   12  H6  UNL     1      -0.813   1.579  -0.578  1.00  0.00           H  
HETATM   13  H7  UNL     1      -0.611   0.924   1.057  1.00  0.00           H  
HETATM   14  H8  UNL     1       1.512   1.628   0.019  1.00  0.00           H  
HETATM   15  H9  UNL     1       1.159   0.679  -1.434  1.00  0.00           H  
HETATM   16  H10 UNL     1       1.379  -1.436  -0.210  1.00  0.00           H  
HETATM   17  H11 UNL     1       1.666  -0.598   1.344  1.00  0.00           H  
HETATM   18  H12 UNL     1       4.196   0.642   0.401  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3   10   11
CONECT    3    4   12   13
CONECT    4    5   14   15
CONECT    5    6   16   17
CONECT    6   18
END
Download

SMILES for HMDB0032457 (1-Pentanethiol)

CCCCCS
Download

INCHI for HMDB0032457 (1-Pentanethiol)

InChI=1S/C5H12S/c1-2-3-4-5-6/h6H,2-5H2,1H3
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
1-MercaptopentaneHMDB
1-PentanthiolHMDB
1-PentylthiolHMDB
Amyl hydrosulfideHMDB
Amyl mercaptanHMDB
Amyl sulfhydrateHMDB
Amyl thioalcoholHMDB
Mercaptan amiliqueHMDB
Mercaptan amyliqueHMDB
N-Amyl mercaptanHMDB
N-Pentyl mercaptanHMDB
N-PentylmercaptanHMDB
N-Thioamyl alcoholHMDB
PentalarmHMDB
Pentane-1-thiolHMDB
PentanethiolHMDB
Pentyl mercaptanHMDB
PentylmercaptanHMDB
Thioamyl alcoholHMDB
Chemical FormulaC5H12S
Average Molecular Weight104.214
Monoisotopic Molecular Weight104.065971074
IUPAC Namepentane-1-thiol
Traditional Name1-pentanethiol
CAS Registry Number110-66-7
SMILES
CCCCCS
InChI Identifier
InChI=1S/C5H12S/c1-2-3-4-5-6/h6H,2-5H2,1H3
InChI KeyZRKMQKLGEQPLNS-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 acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-75.7 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.16 mg/mL at 20 °CNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.62 g/LALOGPS
logP3.02ALOGPS
logP2.5ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)10.2ChemAxon
pKa (Strongest Basic)-9.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity32.76 m³·mol⁻¹ChemAxon
Polarizability13.32 ųChemAxon
Number of Rings0ChemAxon
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]+121.3531661259
DarkChem[M-H]-116.20431661259
DeepCCS[M+H]+131.12630932474
DeepCCS[M-H]-129.03130932474
DeepCCS[M-2H]-164.60130932474
DeepCCS[M+Na]+138.84230932474
AllCCS[M+H]+125.332859911
AllCCS[M+H-H2O]+121.032859911
AllCCS[M+NH4]+129.332859911
AllCCS[M+Na]+130.532859911
AllCCS[M-H]-139.932859911
AllCCS[M+Na-2H]-144.632859911
AllCCS[M+HCOO]-149.732859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1-PentanethiolCCCCCS1060.4Standard polar33892256
1-PentanethiolCCCCCS795.0Standard non polar33892256
1-PentanethiolCCCCCS823.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
1-Pentanethiol,1TMS,isomer #1CCCCCS[Si](C)(C)C1063.0Semi standard non polar33892256
1-Pentanethiol,1TMS,isomer #1CCCCCS[Si](C)(C)C1063.3Standard non polar33892256
1-Pentanethiol,1TBDMS,isomer #1CCCCCS[Si](C)(C)C(C)(C)C1276.7Semi standard non polar33892256
1-Pentanethiol,1TBDMS,isomer #1CCCCCS[Si](C)(C)C(C)(C)C1265.2Standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - 1-Pentanethiol EI-B (Non-derivatized)splash10-0006-9000000000-29c734288b44fcc8d7492017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - 1-Pentanethiol EI-B (Non-derivatized)splash10-0006-9000000000-29c734288b44fcc8d7492018-05-18HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1-Pentanethiol GC-MS (Non-derivatized) - 70eV, Positivesplash10-004l-9000000000-90fc5f1c18f011d778f62017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1-Pentanethiol 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 - 1-Pentanethiol 10V, Positive-QTOFsplash10-0a4i-3900000000-7098d4810c2c7dfb34092016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanethiol 20V, Positive-QTOFsplash10-0ab9-6900000000-2a43f148a7ae75b46fe82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanethiol 40V, Positive-QTOFsplash10-05bf-9000000000-c7d96bd176d68c66afcb2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanethiol 10V, Negative-QTOFsplash10-0udi-3900000000-5911f2263707a054da5b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanethiol 20V, Negative-QTOFsplash10-0udi-4900000000-07f4e50ef64fe8ae574a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanethiol 40V, Negative-QTOFsplash10-001i-9000000000-da9d5ac0df966b26cc742016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanethiol 10V, Positive-QTOFsplash10-00dl-9200000000-5a2be40f527d888617b82021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanethiol 20V, Positive-QTOFsplash10-0006-9000000000-5c59135d55b231a632f42021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanethiol 40V, Positive-QTOFsplash10-0006-9000000000-539706a5477cc25cbf5b2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanethiol 10V, Negative-QTOFsplash10-0udi-0900000000-0a4d8d3d934a27cd2d102021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanethiol 20V, Negative-QTOFsplash10-0udi-0900000000-376ba5d0da5be91cb66c2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanethiol 40V, Negative-QTOFsplash10-001i-9000000000-942ac689538269d6ca7b2021-09-24Wishart 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 IDFDB010034
KNApSAcK IDNot Available
Chemspider ID7776
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound8067
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 References
  1. (). EAFUS: Everything Added to Food in the United States.. .