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Showing metabocard for (±)-2-Pentanethiol (HMDB0041010)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 02:38:31 UTC
Update Date2023-02-21 17:28:32 UTC
HMDB IDHMDB0041010
Secondary Accession Numbers
  • HMDB41010
Metabolite Identification
Common Name(±)-2-Pentanethiol
Description(±)-2-Pentanethiol belongs to the class of organic compounds known as alkylthiols. These are organic compounds containing the thiol functional group linked to an alkyl chain (±)-2-Pentanethiol is a gassy and sulfury tasting compound (±)-2-Pentanethiol has been detected, but not quantified in, guavas (Psidium guajava). This could make (±)-2-pentanethiol a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on (±)-2-Pentanethiol.
Structure
Data?1677000512
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0041010 ((±)-2-Pentanethiol)


  Mrv0541 05061312422D          

  6  5  0  0  0  0            999 V2000
    1.2375    2.1434    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
    0.8250    1.4289    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
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  2  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 HMDB0041010 ((±)-2-Pentanethiol)

HMDB0041010
     RDKit          3D
(±)-2-Pentanethiol
 18 17  0  0  0  0  0  0  0  0999 V2000
    2.4136   -0.2475    0.6480 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0317   -0.6569    0.2293 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2938    0.4980   -0.3968 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0950    0.0562   -0.8086 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9202   -0.4340    0.3380 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9143    1.5198   -1.5298 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.4118    0.2519    1.6350 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0457   -1.1704    0.6415 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8935    0.4572   -0.0756 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4784   -0.9671    1.1606 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9984   -1.5097   -0.4519 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2641    1.4011    0.2124 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8249    0.7729   -1.3472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0780   -0.7109   -1.5937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7723    0.1272    1.2701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8031   -1.5382    0.5109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9985   -0.2979    0.0403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0744    2.4483   -0.4827 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
  4  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
  5 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  0
M  END
Download

3D SDF for HMDB0041010 ((±)-2-Pentanethiol)


  Mrv0541 05061312422D          

  6  5  0  0  0  0            999 V2000
    1.2375    2.1434    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
    0.8250    1.4289    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
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  2  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0041010

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCC(C)S

> <INCHI_IDENTIFIER>
InChI=1S/C5H12S/c1-3-4-5(2)6/h5-6H,3-4H2,1-2H3

> <INCHI_KEY>
QUSTYFNPKBDELJ-UHFFFAOYSA-N

> <FORMULA>
C5H12S

> <MOLECULAR_WEIGHT>
104.214

> <EXACT_MASS>
104.065971074

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
12.96087230019329

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pentane-2-thiol

> <ALOGPS_LOGP>
3.07

> <JCHEM_LOGP>
2.369488402333333

> <ALOGPS_LOGS>
-2.21

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.094798897997482

> <JCHEM_PKA_STRONGEST_BASIC>
-9.665452881055622

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
32.6315

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.45e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-pentanethiol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0041010 ((±)-2-Pentanethiol)

HMDB0041010
     RDKit          3D
(±)-2-Pentanethiol
 18 17  0  0  0  0  0  0  0  0999 V2000
    2.4136   -0.2475    0.6480 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0317   -0.6569    0.2293 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2938    0.4980   -0.3968 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0950    0.0562   -0.8086 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9202   -0.4340    0.3380 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9143    1.5198   -1.5298 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.4118    0.2519    1.6350 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0457   -1.1704    0.6415 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8935    0.4572   -0.0756 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4784   -0.9671    1.1606 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9984   -1.5097   -0.4519 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2641    1.4011    0.2124 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8249    0.7729   -1.3472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0780   -0.7109   -1.5937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7723    0.1272    1.2701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8031   -1.5382    0.5109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9985   -0.2979    0.0403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0744    2.4483   -0.4827 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
  4  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
  5 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  0
M  END
Download

PDB for HMDB0041010 ((±)-2-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       2.310   4.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    6  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
CONECT    1    3                                                            
CONECT    2    5                                                            
CONECT    3    1    4                                                       
CONECT    4    3    5                                                       
CONECT    5    2    4    6                                                  
CONECT    6    5                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
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3D PDB for HMDB0041010 ((±)-2-Pentanethiol)

COMPND    HMDB0041010
HETATM    1  C1  UNL     1       2.414  -0.247   0.648  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.032  -0.657   0.229  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.294   0.498  -0.397  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.095   0.056  -0.809  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.920  -0.434   0.338  1.00  0.00           C  
HETATM    6  S1  UNL     1      -1.914   1.520  -1.530  1.00  0.00           S  
HETATM    7  H1  UNL     1       2.412   0.252   1.635  1.00  0.00           H  
HETATM    8  H2  UNL     1       3.046  -1.170   0.641  1.00  0.00           H  
HETATM    9  H3  UNL     1       2.893   0.457  -0.076  1.00  0.00           H  
HETATM   10  H4  UNL     1       0.478  -0.967   1.161  1.00  0.00           H  
HETATM   11  H5  UNL     1       0.998  -1.510  -0.452  1.00  0.00           H  
HETATM   12  H6  UNL     1       0.264   1.401   0.212  1.00  0.00           H  
HETATM   13  H7  UNL     1       0.825   0.773  -1.347  1.00  0.00           H  
HETATM   14  H8  UNL     1      -1.078  -0.711  -1.594  1.00  0.00           H  
HETATM   15  H9  UNL     1      -1.772   0.127   1.270  1.00  0.00           H  
HETATM   16  H10 UNL     1      -1.803  -1.538   0.511  1.00  0.00           H  
HETATM   17  H11 UNL     1      -2.999  -0.298   0.040  1.00  0.00           H  
HETATM   18  H12 UNL     1      -2.074   2.448  -0.483  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3   10   11
CONECT    3    4   12   13
CONECT    4    5    6   14
CONECT    5   15   16   17
CONECT    6   18
END
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SMILES for HMDB0041010 ((±)-2-Pentanethiol)

CCCC(C)S
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INCHI for HMDB0041010 ((±)-2-Pentanethiol)

InChI=1S/C5H12S/c1-3-4-5(2)6/h5-6H,3-4H2,1-2H3
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC5H12S
Average Molecular Weight104.214
Monoisotopic Molecular Weight104.065971074
IUPAC Namepentane-2-thiol
Traditional Name2-pentanethiol
CAS Registry Number110503-18-9
SMILES
CCCC(C)S
InChI Identifier
InChI=1S/C5H12S/c1-3-4-5(2)6/h5-6H,3-4H2,1-2H3
InChI KeyQUSTYFNPKBDELJ-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 effectNot Available
Disposition
Biological location
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
Water Solubility0.64 g/LALOGPS
logP3.07ALOGPS
logP2.37ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)10.09ChemAxon
pKa (Strongest Basic)-9.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity32.63 m³·mol⁻¹ChemAxon
Polarizability12.96 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]+120.52631661259
DarkChem[M-H]-115.93231661259
DeepCCS[M+H]+132.23930932474
DeepCCS[M-H]-130.16230932474
DeepCCS[M-2H]-165.82830932474
DeepCCS[M+Na]+140.6530932474
AllCCS[M+H]+125.132859911
AllCCS[M+H-H2O]+120.832859911
AllCCS[M+NH4]+129.232859911
AllCCS[M+Na]+130.332859911
AllCCS[M-H]-138.932859911
AllCCS[M+Na-2H]-143.632859911
AllCCS[M+HCOO]-148.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
(??)-2-PentanethiolCCCC(C)S966.0Standard polar33892256
(??)-2-PentanethiolCCCC(C)S739.0Standard non polar33892256
(??)-2-PentanethiolCCCC(C)S766.9Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
(±)-2-Pentanethiol,1TMS,isomer #1CCCC(C)S[Si](C)(C)C995.9Semi standard non polar33892256
(±)-2-Pentanethiol,1TMS,isomer #1CCCC(C)S[Si](C)(C)C1004.6Standard non polar33892256
(±)-2-Pentanethiol,1TBDMS,isomer #1CCCC(C)S[Si](C)(C)C(C)(C)C1215.7Semi standard non polar33892256
(±)-2-Pentanethiol,1TBDMS,isomer #1CCCC(C)S[Si](C)(C)C(C)(C)C1221.2Standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - (±)-2-Pentanethiol GC-MS (Non-derivatized) - 70eV, Positivesplash10-0203-9000000000-76363e8d248cb235200e2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - (±)-2-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 - (±)-2-Pentanethiol 10V, Positive-QTOFsplash10-0a4i-3900000000-883cad731ae52dcd01d82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (±)-2-Pentanethiol 20V, Positive-QTOFsplash10-0a4i-3900000000-a5979de06a53924407d22016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (±)-2-Pentanethiol 40V, Positive-QTOFsplash10-05fu-9000000000-77892984ddc60fbceab12016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (±)-2-Pentanethiol 10V, Negative-QTOFsplash10-0udi-1900000000-21d0aee0980c5812dc202016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (±)-2-Pentanethiol 20V, Negative-QTOFsplash10-0udi-2900000000-ec32d587eecea98ac8c52016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (±)-2-Pentanethiol 40V, Negative-QTOFsplash10-001i-9000000000-35bd47dd39cdf40c6fde2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (±)-2-Pentanethiol 10V, Positive-QTOFsplash10-00dl-9200000000-4e3a7627bd5aec372fc72021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (±)-2-Pentanethiol 20V, Positive-QTOFsplash10-0006-9000000000-a1c72fcd8e45f0c0d14a2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (±)-2-Pentanethiol 40V, Positive-QTOFsplash10-03dl-9000000000-bf6d73cb95af7f7efa652021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (±)-2-Pentanethiol 10V, Negative-QTOFsplash10-0udi-0900000000-0a4d8d3d934a27cd2d102021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (±)-2-Pentanethiol 20V, Negative-QTOFsplash10-0udi-0900000000-601da8d9a096e5f8ee212021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (±)-2-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 IDFDB020872
KNApSAcK IDNot Available
Chemspider ID56209
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound62424
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. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .