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Showing metabocard for 2-Pyridinemethanethiol (HMDB0041346)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 03:01:09 UTC
Update Date2023-02-21 17:28:39 UTC
HMDB IDHMDB0041346
Secondary Accession Numbers
  • HMDB41346
Metabolite Identification
Common Name2-Pyridinemethanethiol
Description2-Pyridinemethanethiol 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. 2-Pyridinemethanethiol is a beef, meaty, and roasted tasting compound. Based on a literature review very few articles have been published on 2-Pyridinemethanethiol.
Structure
Data?1677000519
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0041346 (2-Pyridinemethanethiol)

  Mrv0541 05061312362D          

  8  8  0  0  0  0            999 V2000
    0.0000    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    0.8250    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    2.0625    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
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  6  3  2  0  0  0  0
  6  5  1  0  0  0  0
  7  4  2  0  0  0  0
  7  6  1  0  0  0  0
  8  5  1  0  0  0  0
M  END
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3D MOL for HMDB0041346 (2-Pyridinemethanethiol)

HMDB0041346
     RDKit          3D
2-Pyridinemethanethiol
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.8795    1.1191   -0.4312 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.9951   -0.4663   -0.4064 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5297   -0.2797   -0.2388 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0169   -0.2515    1.0288 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3379   -0.0791    1.1878 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1645    0.0626    0.1005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5939    0.0264   -1.1504 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2679   -0.1420   -1.3189 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0288    2.1699    0.0113 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3720   -1.1490    0.3582 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1433   -0.9342   -1.4028 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7001   -0.3667    1.8658 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7651   -0.0538    2.1822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2533    0.2016    0.2128 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2827    0.1427   -1.9990 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  3  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  4 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  0
M  END
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3D SDF for HMDB0041346 (2-Pyridinemethanethiol)

  Mrv0541 05061312362D          

  8  8  0  0  0  0            999 V2000
    0.0000    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    0.8250    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    2.0625    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
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  6  3  2  0  0  0  0
  6  5  1  0  0  0  0
  7  4  2  0  0  0  0
  7  6  1  0  0  0  0
  8  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0041346

> <DATABASE_NAME>
hmdb

> <SMILES>
SCC1=CC=CC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C6H7NS/c8-5-6-3-1-2-4-7-6/h1-4,8H,5H2

> <INCHI_KEY>
SJIIDWBFRZACDQ-UHFFFAOYSA-N

> <FORMULA>
C6H7NS

> <MOLECULAR_WEIGHT>
125.191

> <EXACT_MASS>
125.029919919

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
13.323027464332796

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyridin-2-ylmethanethiol

> <ALOGPS_LOGP>
1.46

> <JCHEM_LOGP>
1.113508979333333

> <ALOGPS_LOGS>
-1.87

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.760212093526349

> <JCHEM_PKA_STRONGEST_BASIC>
4.936831411436465

> <JCHEM_POLAR_SURFACE_AREA>
12.89

> <JCHEM_REFRACTIVITY>
36.321799999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.68e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-pyridinemethanethiol

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0041346 (2-Pyridinemethanethiol)

HMDB0041346
     RDKit          3D
2-Pyridinemethanethiol
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.8795    1.1191   -0.4312 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.9951   -0.4663   -0.4064 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5297   -0.2797   -0.2388 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0169   -0.2515    1.0288 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3379   -0.0791    1.1878 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1645    0.0626    0.1005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5939    0.0264   -1.1504 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2679   -0.1420   -1.3189 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0288    2.1699    0.0113 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3720   -1.1490    0.3582 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1433   -0.9342   -1.4028 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7001   -0.3667    1.8658 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7651   -0.0538    2.1822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2533    0.2016    0.2128 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2827    0.1427   -1.9990 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  3  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  4 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  0
M  END
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PDB for HMDB0041346 (2-Pyridinemethanethiol)

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       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   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   3.850   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  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM    8  S   UNK     0       0.000   4.620   0.000  0.00  0.00           S+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    6                                                       
CONECT    4    2    7                                                       
CONECT    5    6    8                                                       
CONECT    6    3    5    7                                                  
CONECT    7    4    6                                                       
CONECT    8    5                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0041346 (2-Pyridinemethanethiol)

COMPND    HMDB0041346
HETATM    1  S1  UNL     1       2.880   1.119  -0.431  1.00  0.00           S  
HETATM    2  C1  UNL     1       1.995  -0.466  -0.406  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.530  -0.280  -0.239  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.017  -0.252   1.029  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.338  -0.079   1.188  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.164   0.063   0.100  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.594   0.026  -1.150  1.00  0.00           C  
HETATM    8  N1  UNL     1      -0.268  -0.142  -1.319  1.00  0.00           N  
HETATM    9  H1  UNL     1       2.029   2.170   0.011  1.00  0.00           H  
HETATM   10  H2  UNL     1       2.372  -1.149   0.358  1.00  0.00           H  
HETATM   11  H3  UNL     1       2.143  -0.934  -1.403  1.00  0.00           H  
HETATM   12  H4  UNL     1       0.700  -0.367   1.866  1.00  0.00           H  
HETATM   13  H5  UNL     1      -1.765  -0.054   2.182  1.00  0.00           H  
HETATM   14  H6  UNL     1      -3.253   0.202   0.213  1.00  0.00           H  
HETATM   15  H7  UNL     1      -2.283   0.143  -1.999  1.00  0.00           H  
CONECT    1    2    9
CONECT    2    3   10   11
CONECT    3    4    4    8
CONECT    4    5   12
CONECT    5    6    6   13
CONECT    6    7   14
CONECT    7    8    8   15
END
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SMILES for HMDB0041346 (2-Pyridinemethanethiol)

SCC1=CC=CC=N1
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INCHI for HMDB0041346 (2-Pyridinemethanethiol)

InChI=1S/C6H7NS/c8-5-6-3-1-2-4-7-6/h1-4,8H,5H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-(Mercaptomethyl)pyridineHMDB
2-(Thiomethyl)pyridineHMDB
2-PicolylthiolHMDB
2-PyridinylmethanethiolHMDB
2-Pyridinylmethyl mercaptanHMDB
2-Pyridylmethyl mercaptanHMDB
FEMA 3232HMDB
Pyridine-2-thiocarbinolHMDB
Chemical FormulaC6H7NS
Average Molecular Weight125.191
Monoisotopic Molecular Weight125.029919919
IUPAC Namepyridin-2-ylmethanethiol
Traditional Name2-pyridinemethanethiol
CAS Registry Number2044-73-7
SMILES
SCC1=CC=CC=N1
InChI Identifier
InChI=1S/C6H7NS/c8-5-6-3-1-2-4-7-6/h1-4,8H,5H2
InChI KeySJIIDWBFRZACDQ-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 effect
Organoleptic effect
Disposition
Biological locationSource
ProcessNot Available
Role
Industrial applicationBiological role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point57.00 to 58.00 °C. @ 0.60 mm HgThe Good Scents Company Information System
Water Solubility149900 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP1.355 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
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 IDFDB021269
KNApSAcK IDNot Available
Chemspider ID224560
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound256071
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1035641
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.. .