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Showing metabocard for 2-Mercaptopyridine (HMDB0245194)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:17:21 UTC
Update Date2021-09-26 22:53:31 UTC
HMDB IDHMDB0245194
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-Mercaptopyridine
Description2-Mercaptopyridine, also known as 2-pyridinethiol or 2-thiopyridone, belongs to the class of organic compounds known as dihydropyridines. Dihydropyridines are compounds containing a dihydropyridine moiety, which is a semi-saturated pyridine derivative with two double bonds. Based on a literature review a small amount of articles have been published on 2-Mercaptopyridine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2-mercaptopyridine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2-Mercaptopyridine 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 HMDB0245194 (2-Mercaptopyridine)


  Mrv0541 02231216522D          

  7  7  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 S   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
    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 C   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 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
M  END
Download

3D MOL for HMDB0245194 (2-Mercaptopyridine)

HMDB0245194
     RDKit          3D
2-Mercaptopyridine
 12 12  0  0  0  0  0  0  0  0999 V2000
    2.8987   -0.1685   -0.0001 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.1260    0.0271    0.0132 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3337   -1.1023    0.0206 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0440   -1.0523    0.0310 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6470    0.1868    0.0341 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8343    1.3018    0.0265 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5095    1.2137    0.0164 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5663    1.0186   -0.2680 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8177   -2.0707    0.0181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6620   -1.9347    0.0369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7317    0.2996    0.0422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3330    2.2809    0.0291 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
  5  6  1  0
  6  7  2  0
  7  2  1  0
  1  8  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  6 12  1  0
M  END
Download

3D SDF for HMDB0245194 (2-Mercaptopyridine)


  Mrv0541 02231216522D          

  7  7  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 S   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
    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 C   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 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245194

> <DATABASE_NAME>
hmdb

> <SMILES>
SC1=CC=CC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C5H5NS/c7-5-3-1-2-4-6-5/h1-4H,(H,6,7)

> <INCHI_KEY>
WHMDPDGBKYUEMW-UHFFFAOYSA-N

> <FORMULA>
C5H5NS

> <MOLECULAR_WEIGHT>
111.165

> <EXACT_MASS>
111.014269855

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
11.336436632525599

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyridine-2-thiol

> <ALOGPS_LOGP>
1.24

> <JCHEM_LOGP>
1.4432380986666666

> <ALOGPS_LOGS>
-1.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.635218176212668

> <JCHEM_PKA_STRONGEST_BASIC>
0.5023079647290206

> <JCHEM_POLAR_SURFACE_AREA>
12.89

> <JCHEM_REFRACTIVITY>
32.224399999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.37e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-pyridinethiol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0245194 (2-Mercaptopyridine)

HMDB0245194
     RDKit          3D
2-Mercaptopyridine
 12 12  0  0  0  0  0  0  0  0999 V2000
    2.8987   -0.1685   -0.0001 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.1260    0.0271    0.0132 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3337   -1.1023    0.0206 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0440   -1.0523    0.0310 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6470    0.1868    0.0341 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8343    1.3018    0.0265 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5095    1.2137    0.0164 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5663    1.0186   -0.2680 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8177   -2.0707    0.0181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6620   -1.9347    0.0369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7317    0.2996    0.0422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3330    2.2809    0.0291 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
  5  6  1  0
  6  7  2  0
  7  2  1  0
  1  8  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  6 12  1  0
M  END
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PDB for HMDB0245194 (2-Mercaptopyridine)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  S   UNK     0       1.334   3.850   0.000  0.00  0.00           S+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0245194 (2-Mercaptopyridine)

COMPND    HMDB0245194
HETATM    1  S1  UNL     1       2.899  -0.169  -0.000  1.00  0.00           S  
HETATM    2  C1  UNL     1       1.126   0.027   0.013  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.334  -1.102   0.021  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.044  -1.052   0.031  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.647   0.187   0.034  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.834   1.302   0.027  1.00  0.00           C  
HETATM    7  N1  UNL     1       0.509   1.214   0.016  1.00  0.00           N  
HETATM    8  H1  UNL     1       3.566   1.019  -0.268  1.00  0.00           H  
HETATM    9  H2  UNL     1       0.818  -2.071   0.018  1.00  0.00           H  
HETATM   10  H3  UNL     1      -1.662  -1.935   0.037  1.00  0.00           H  
HETATM   11  H4  UNL     1      -2.732   0.300   0.042  1.00  0.00           H  
HETATM   12  H5  UNL     1      -1.333   2.281   0.029  1.00  0.00           H  
CONECT    1    2    8
CONECT    2    3    3    7
CONECT    3    4    9
CONECT    4    5    5   10
CONECT    5    6   11
CONECT    6    7    7   12
END
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SMILES for HMDB0245194 (2-Mercaptopyridine)

SC1=CC=CC=N1
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INCHI for HMDB0245194 (2-Mercaptopyridine)

InChI=1S/C5H5NS/c7-5-3-1-2-4-6-5/h1-4H,(H,6,7)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-PyridinethiolChEBI
2-PyridinylthiolChEBI
2-PyridylthiolChEBI
2-ThiopyridineHMDB
2-Thiopyridine zinc saltHMDB
2-Thiopyridine sodium saltHMDB
Pyridine-2-thioneHMDB
2-Thiopyridine lead salt (+2)HMDB
2-Thiopyridine titanium salt (+1)HMDB
2-ThiopyridoneHMDB
2-MercaptopyridineChEBI
Chemical FormulaC5H5NS
Average Molecular Weight111.165
Monoisotopic Molecular Weight111.014269855
IUPAC Namepyridine-2-thiol
Traditional Name2-pyridinethiol
CAS Registry NumberNot Available
SMILES
SC1=CC=CC=N1
InChI Identifier
InChI=1S/C5H5NS/c7-5-3-1-2-4-6-5/h1-4H,(H,6,7)
InChI KeyWHMDPDGBKYUEMW-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dihydropyridines. Dihydropyridines are compounds containing a dihydropyridine moiety, which is a semi-saturated pyridine derivative with two double bonds.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassHydropyridines
Direct ParentDihydropyridines
Alternative Parents
Substituents
  • Dihydropyridine
  • Heteroaromatic compound
  • Thiolactam
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organosulfur compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
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
logP1.24ALOGPS
logP1.44ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)7.64ChemAxon
pKa (Strongest Basic)0.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area12.89 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity32.22 m³·mol⁻¹ChemAxon
Polarizability11.34 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]+123.10130932474
DeepCCS[M-H]-120.30130932474
DeepCCS[M-2H]-156.6130932474
DeepCCS[M+Na]+131.43930932474
AllCCS[M+H]+120.632859911
AllCCS[M+H-H2O]+115.532859911
AllCCS[M+NH4]+125.432859911
AllCCS[M+Na]+126.832859911
AllCCS[M-H]-120.232859911
AllCCS[M+Na-2H]-123.332859911
AllCCS[M+HCOO]-126.632859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-MercaptopyridineSC1=CC=CC=N11691.4Standard polar33892256
2-MercaptopyridineSC1=CC=CC=N11087.4Standard non polar33892256
2-MercaptopyridineSC1=CC=CC=N11190.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-Mercaptopyridine,1TMS,isomer #1C[Si](C)(C)SC1=CC=CC=N11233.3Semi standard non polar33892256
2-Mercaptopyridine,1TMS,isomer #1C[Si](C)(C)SC1=CC=CC=N11170.3Standard non polar33892256
2-Mercaptopyridine,1TMS,isomer #1C[Si](C)(C)SC1=CC=CC=N11468.8Standard polar33892256
2-Mercaptopyridine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SC1=CC=CC=N11513.0Semi standard non polar33892256
2-Mercaptopyridine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SC1=CC=CC=N11397.3Standard non polar33892256
2-Mercaptopyridine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SC1=CC=CC=N11646.2Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2-Mercaptopyridine GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-9500000000-0e9366d4cafd247987db2017-08-28Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Mercaptopyridine 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-Mercaptopyridine 10V, Positive-QTOFsplash10-03di-1900000000-3bead07463c720ce1b012017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Mercaptopyridine 20V, Positive-QTOFsplash10-0ik9-9600000000-f88a8df95eb9392c9e6e2017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Mercaptopyridine 40V, Positive-QTOFsplash10-0udi-9000000000-5a02ad9ef9439a60e7a12017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Mercaptopyridine 10V, Negative-QTOFsplash10-03di-0900000000-4bc488165343ec8d2add2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Mercaptopyridine 20V, Negative-QTOFsplash10-03di-1900000000-28aa70cbd9f67e5dad7b2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Mercaptopyridine 40V, Negative-QTOFsplash10-0a59-9100000000-64e2834ed7fef999f85e2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Mercaptopyridine 10V, Positive-QTOFsplash10-03di-0900000000-0e787e112dfa8e771f852021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Mercaptopyridine 20V, Positive-QTOFsplash10-03di-8900000000-da67ad539513a101c24c2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Mercaptopyridine 40V, Positive-QTOFsplash10-0udi-9000000000-6c6656f1050eae2e71632021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Mercaptopyridine 10V, Negative-QTOFsplash10-03di-1900000000-bfe8e9b7523ccd8d2d972021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Mercaptopyridine 20V, Negative-QTOFsplash10-03di-0900000000-6a0cec2dc058adc748602021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Mercaptopyridine 40V, Negative-QTOFsplash10-0bt9-9300000000-be0838df17f90b339d502021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-12Wishart 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 IDDB03329
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID2005897
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link2-Mercaptopyridine
METLIN IDNot Available
PubChem Compound17523
PDB IDNot Available
ChEBI ID45223
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 ]