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Showing metabocard for 4-Pyridylethylmercaptan (HMDB0246578)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:35:41 UTC
Update Date2021-09-26 22:55:45 UTC
HMDB IDHMDB0246578
Secondary Accession NumbersNone
Metabolite Identification
Common Name4-Pyridylethylmercaptan
Description4-Pyridylethylmercaptan, also known as 4-pyridoethanethiol, belongs to the class of organic compounds known as pyridines and derivatives. Pyridines and derivatives are compounds containing a pyridine ring, which is a six-member aromatic heterocycle which consists of one nitrogen atom and five carbon atoms. Based on a literature review very few articles have been published on 4-Pyridylethylmercaptan. This compound has been identified in human blood as reported by (PMID: 31557052 ). 4-pyridylethylmercaptan is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 4-Pyridylethylmercaptan is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0246578 (4-Pyridylethylmercaptan)


  Mrv1652309112101352D          

  9  9  0  0  0  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
M  END
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3D MOL for HMDB0246578 (4-Pyridylethylmercaptan)

HMDB0246578
     RDKit          3D
4-Pyridylethylmercaptan
 18 18  0  0  0  0  0  0  0  0999 V2000
    3.6527    0.7566   -0.0187 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.8699    0.8786    0.2916 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1474   -0.2385   -0.4151 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3030   -0.2185   -0.2187 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8453   -0.9056    0.8485 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2038   -0.9248    1.0868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9845   -0.2340    0.2196 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4992    0.4371   -0.8159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1539    0.4681   -1.0690 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0621   -0.5240    0.4374 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6129    0.9750    1.3425 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5367    1.8340   -0.2130 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3341   -0.1984   -1.5117 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5356   -1.1937   -0.0045 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2159   -1.4658    1.5523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6617   -1.4532    1.9139 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1554    0.9905   -1.5059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7286    1.0169   -1.9203 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  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9  4  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  5 15  1  0
  6 16  1  0
  8 17  1  0
  9 18  1  0
M  END
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3D SDF for HMDB0246578 (4-Pyridylethylmercaptan)


  Mrv1652309112101352D          

  9  9  0  0  0  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246578

> <DATABASE_NAME>
hmdb

> <SMILES>
SCCC1=CC=NC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C7H9NS/c9-6-3-7-1-4-8-5-2-7/h1-2,4-5,9H,3,6H2

> <INCHI_KEY>
VBAOEVKQBLGWTH-UHFFFAOYSA-N

> <FORMULA>
C7H9NS

> <MOLECULAR_WEIGHT>
139.22

> <EXACT_MASS>
139.045570468

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
15.331009547480477

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(pyridin-4-yl)ethane-1-thiol

> <ALOGPS_LOGP>
1.74

> <JCHEM_LOGP>
1.5282542226666667

> <ALOGPS_LOGS>
-2.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.161304246693106

> <JCHEM_PKA_STRONGEST_BASIC>
5.624493758205912

> <JCHEM_POLAR_SURFACE_AREA>
12.89

> <JCHEM_REFRACTIVITY>
41.500600000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.90e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(pyridin-4-yl)ethanethiol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0246578 (4-Pyridylethylmercaptan)

HMDB0246578
     RDKit          3D
4-Pyridylethylmercaptan
 18 18  0  0  0  0  0  0  0  0999 V2000
    3.6527    0.7566   -0.0187 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.8699    0.8786    0.2916 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1474   -0.2385   -0.4151 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3030   -0.2185   -0.2187 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8453   -0.9056    0.8485 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2038   -0.9248    1.0868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9845   -0.2340    0.2196 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4992    0.4371   -0.8159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1539    0.4681   -1.0690 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0621   -0.5240    0.4374 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6129    0.9750    1.3425 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5367    1.8340   -0.2130 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3341   -0.1984   -1.5117 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5356   -1.1937   -0.0045 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2159   -1.4658    1.5523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6617   -1.4532    1.9139 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1554    0.9905   -1.5059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7286    1.0169   -1.9203 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  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9  4  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  5 15  1  0
  6 16  1  0
  8 17  1  0
  9 18  1  0
M  END
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PDB for HMDB0246578 (4-Pyridylethylmercaptan)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    9  S   UNK     0       2.667   6.160   0.000  0.00  0.00           S+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for HMDB0246578 (4-Pyridylethylmercaptan)

COMPND    HMDB0246578
HETATM    1  S1  UNL     1       3.653   0.757  -0.019  1.00  0.00           S  
HETATM    2  C1  UNL     1       1.870   0.879   0.292  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.147  -0.239  -0.415  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.303  -0.219  -0.219  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.845  -0.906   0.849  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.204  -0.925   1.087  1.00  0.00           C  
HETATM    7  N1  UNL     1      -2.985  -0.234   0.220  1.00  0.00           N  
HETATM    8  C6  UNL     1      -2.499   0.437  -0.816  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.154   0.468  -1.069  1.00  0.00           C  
HETATM   10  H1  UNL     1       4.062  -0.524   0.437  1.00  0.00           H  
HETATM   11  H2  UNL     1       1.613   0.975   1.343  1.00  0.00           H  
HETATM   12  H3  UNL     1       1.537   1.834  -0.213  1.00  0.00           H  
HETATM   13  H4  UNL     1       1.334  -0.198  -1.512  1.00  0.00           H  
HETATM   14  H5  UNL     1       1.536  -1.194  -0.004  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.216  -1.466   1.552  1.00  0.00           H  
HETATM   16  H7  UNL     1      -2.662  -1.453   1.914  1.00  0.00           H  
HETATM   17  H8  UNL     1      -3.155   0.990  -1.506  1.00  0.00           H  
HETATM   18  H9  UNL     1      -0.729   1.017  -1.920  1.00  0.00           H  
CONECT    1    2   10
CONECT    2    3   11   12
CONECT    3    4   13   14
CONECT    4    5    5    9
CONECT    5    6   15
CONECT    6    7    7   16
CONECT    7    8
CONECT    8    9    9   17
CONECT    9   18
END
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SMILES for HMDB0246578 (4-Pyridylethylmercaptan)

SCCC1=CC=NC=C1
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INCHI for HMDB0246578 (4-Pyridylethylmercaptan)

InChI=1S/C7H9NS/c9-6-3-7-1-4-8-5-2-7/h1-2,4-5,9H,3,6H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
4-PyridoethanethiolMeSH
Chemical FormulaC7H9NS
Average Molecular Weight139.22
Monoisotopic Molecular Weight139.045570468
IUPAC Name2-(pyridin-4-yl)ethane-1-thiol
Traditional Name2-(pyridin-4-yl)ethanethiol
CAS Registry NumberNot Available
SMILES
SCCC1=CC=NC=C1
InChI Identifier
InChI=1S/C7H9NS/c9-6-3-7-1-4-8-5-2-7/h1-2,4-5,9H,3,6H2
InChI KeyVBAOEVKQBLGWTH-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyridines and derivatives. Pyridines and derivatives are compounds containing a pyridine ring, which is a six-member aromatic heterocycle which consists of one nitrogen atom and five carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassNot Available
Direct ParentPyridines and derivatives
Alternative Parents
Substituents
  • Pyridine
  • Heteroaromatic compound
  • Azacycle
  • Alkylthiol
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organosulfur compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic 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
logP1.74ALOGPS
logP1.53ChemAxon
logS-2.4ALOGPS
pKa (Strongest Acidic)10.16ChemAxon
pKa (Strongest Basic)5.62ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area12.89 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity41.5 m³·mol⁻¹ChemAxon
Polarizability15.33 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
DeepCCS[M+H]+125.7930932474
DeepCCS[M-H]-122.66430932474
DeepCCS[M-2H]-159.52830932474
DeepCCS[M+Na]+134.48930932474
AllCCS[M+H]+128.432859911
AllCCS[M+H-H2O]+123.832859911
AllCCS[M+NH4]+132.732859911
AllCCS[M+Na]+134.032859911
AllCCS[M-H]-129.532859911
AllCCS[M+Na-2H]-131.732859911
AllCCS[M+HCOO]-134.132859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
4-PyridylethylmercaptanSCCC1=CC=NC=C11892.8Standard polar33892256
4-PyridylethylmercaptanSCCC1=CC=NC=C11245.1Standard non polar33892256
4-PyridylethylmercaptanSCCC1=CC=NC=C11275.0Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
4-Pyridylethylmercaptan,1TMS,isomer #1C[Si](C)(C)SCCC1=CC=NC=C11516.2Semi standard non polar33892256
4-Pyridylethylmercaptan,1TMS,isomer #1C[Si](C)(C)SCCC1=CC=NC=C11438.1Standard non polar33892256
4-Pyridylethylmercaptan,1TMS,isomer #1C[Si](C)(C)SCCC1=CC=NC=C11794.8Standard polar33892256
4-Pyridylethylmercaptan,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SCCC1=CC=NC=C11751.1Semi standard non polar33892256
4-Pyridylethylmercaptan,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SCCC1=CC=NC=C11682.1Standard non polar33892256
4-Pyridylethylmercaptan,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SCCC1=CC=NC=C11932.5Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 4-Pyridylethylmercaptan GC-MS (Non-derivatized) - 70eV, Positivesplash10-052f-9500000000-452961168c6cd77bab3a2021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 4-Pyridylethylmercaptan 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 - 4-Pyridylethylmercaptan 10V, Positive-QTOFsplash10-0a4i-0900000000-e958211e5e18ea3dfa2d2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Pyridylethylmercaptan 20V, Positive-QTOFsplash10-0a4i-2900000000-0688db3fa68c3d42313d2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Pyridylethylmercaptan 40V, Positive-QTOFsplash10-004l-9100000000-a11ebe5161939ff757012021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Pyridylethylmercaptan 10V, Negative-QTOFsplash10-000i-0900000000-f8050d4d090a970d1c9e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Pyridylethylmercaptan 20V, Negative-QTOFsplash10-000i-1900000000-d3e012345c20da961f1f2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Pyridylethylmercaptan 40V, Negative-QTOFsplash10-001i-9000000000-ebad4238928d6f979b302021-10-12Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID133065
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound150969
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. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]