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Showing metabocard for Pyridine (HMDB0000926)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:18 UTC
HMDB IDHMDB0000926
Secondary Accession Numbers
  • HMDB00926
Metabolite Identification
Common NamePyridine
DescriptionPyridine is a clear liquid with an odor that is sour, putrid, and fish-like. It is a relatively simple heterocyclic aromatic organic compound that is structurally related to benzene, with one CH group in the six-membered ring replaced by a nitrogen atom. Pyridine is obtained from crude coal tar or is synthesized from acetaldehyde, formaldehyde and ammonia. Pyridine is often used as a denaturant for antifreeze mixtures, for ethyl alcohol, for fungicides, and as a dyeing aid for textiles. It is a harmful substance if inhaled, ingested or absorbed through the skin. In particular, it is known to reduce male fertility and is considered carcinogenic. Common symptoms of acute exposure to pyridine include: headache, coughing, asthmatic breathing, laryngitis, nausea and vomiting. -- Wikipedia .
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000926 (Pyridine)

  Mrv1652304272018112D          

  6  6  0  0  0  0            999 V2000
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  2  0  0  0  0
  4  6  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
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3D MOL for HMDB0000926 (Pyridine)

HMDB0000926
     RDKit          3D
Pyridine
 11 11  0  0  0  0  0  0  0  0999 V2000
    1.0148   -0.5603    0.0130 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1706   -1.2627    0.0044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3708   -0.5981   -0.0110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3591    0.7422   -0.0174 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2388    1.4753   -0.0095 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9686    0.8183    0.0059 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9680   -1.0578    0.0251 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1601   -2.3507    0.0097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2904   -1.1861   -0.0175 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2424    2.5642   -0.0149 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8808    1.4157    0.0122 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  1  1  0
  1  7  1  0
  2  8  1  0
  3  9  1  0
  5 10  1  0
  6 11  1  0
M  END
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3D SDF for HMDB0000926 (Pyridine)

  Mrv1652304272018112D          

  6  6  0  0  0  0            999 V2000
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  2  0  0  0  0
  4  6  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000926

> <DATABASE_NAME>
hmdb

> <SMILES>
C1=CC=NC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H

> <INCHI_KEY>
JUJWROOIHBZHMG-UHFFFAOYSA-N

> <FORMULA>
C5H5N

> <MOLECULAR_WEIGHT>
79.0999

> <EXACT_MASS>
79.042199165

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
8.249444777134816

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyridine

> <ALOGPS_LOGP>
0.70

> <JCHEM_LOGP>
0.7555733889999999

> <ALOGPS_LOGS>
0.49

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
5.118161478418525

> <JCHEM_POLAR_SURFACE_AREA>
12.89

> <JCHEM_REFRACTIVITY>
23.901099999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.42e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyridine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0000926 (Pyridine)

HMDB0000926
     RDKit          3D
Pyridine
 11 11  0  0  0  0  0  0  0  0999 V2000
    1.0148   -0.5603    0.0130 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1706   -1.2627    0.0044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3708   -0.5981   -0.0110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3591    0.7422   -0.0174 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2388    1.4753   -0.0095 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9686    0.8183    0.0059 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9680   -1.0578    0.0251 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1601   -2.3507    0.0097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2904   -1.1861   -0.0175 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2424    2.5642   -0.0149 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8808    1.4157    0.0122 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  1  1  0
  1  7  1  0
  2  8  1  0
  3  9  1  0
  5 10  1  0
  6 11  1  0
M  END
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PDB for HMDB0000926 (Pyridine)

HEADER    PROTEIN                                 27-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-APR-20         0                                  
HETATM    1  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.770   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -1.540   0.000   0.000  0.00  0.00           N+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    6                                                       
CONECT    6    4    5                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0000926 (Pyridine)

COMPND    HMDB0000926
HETATM    1  C1  UNL     1       1.015  -0.560   0.013  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.171  -1.263   0.004  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.371  -0.598  -0.011  1.00  0.00           C  
HETATM    4  N1  UNL     1      -1.359   0.742  -0.017  1.00  0.00           N  
HETATM    5  C4  UNL     1      -0.239   1.475  -0.010  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.969   0.818   0.006  1.00  0.00           C  
HETATM    7  H1  UNL     1       1.968  -1.058   0.025  1.00  0.00           H  
HETATM    8  H2  UNL     1      -0.160  -2.351   0.010  1.00  0.00           H  
HETATM    9  H3  UNL     1      -2.290  -1.186  -0.017  1.00  0.00           H  
HETATM   10  H4  UNL     1      -0.242   2.564  -0.015  1.00  0.00           H  
HETATM   11  H5  UNL     1       1.881   1.416   0.012  1.00  0.00           H  
CONECT    1    2    2    6    7
CONECT    2    3    8
CONECT    3    4    4    9
CONECT    4    5
CONECT    5    6    6   10
CONECT    6   11
END
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SMILES for HMDB0000926 (Pyridine)

C1=CC=NC=C1
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INCHI for HMDB0000926 (Pyridine)

InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H
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View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC5H5N
Average Molecular Weight79.0999
Monoisotopic Molecular Weight79.042199165
IUPAC Namepyridine
Traditional Namepyridine
CAS Registry Number110-86-1
SMILES
C1=CC=NC=C1
InChI Identifier
InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H
InChI KeyJUJWROOIHBZHMG-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
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Environmental roleIndustrial applicationBiological role
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-42 °CNot Available
Boiling Point115.00 to 116.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility1000 mg/mLNot Available
LogP0.65HANSCH,C ET AL. (1995)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Feces
Tissue Locations
  • Brain
  • Epidermis
  • Fibroblasts
  • Intestine
  • Kidney
  • Liver
  • Neuron
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Campylobacter jejuni infection		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Clostridium difficile infection		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Ulcerative Colitis		 details
Associated Disorders and Diseases
Disease References
Ulcerative colitis
  1. Garner CE, Smith S, de Lacy Costello B, White P, Spencer R, Probert CS, Ratcliffe NM: Volatile organic compounds from feces and their potential for diagnosis of gastrointestinal disease. FASEB J. 2007 Jun;21(8):1675-88. Epub 2007 Feb 21. [PubMed:17314143 ]
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB014733
KNApSAcK IDC00053734
Chemspider ID1020
KEGG Compound IDC00747
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPyridine
METLIN ID5877
PubChem Compound1049
PDB IDNot Available
ChEBI ID16227
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1009251
References
Synthesis ReferenceLi, Jian; Ma, Xibo; Zhao, Ming; Yao, Jun; Ma, Chenyang; Wang, Ping; Wang, Xiaonan; Liu, Qingpei. Method for manufacturing pyridine with >99% purity. Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 4pp.
Material Safety Data Sheet (MSDS)Not Available
General References

Enzymes

Enzyme Details
1. Nicotinate-nucleotide pyrophosphorylase [carboxylating]
General function:
Involved in catalytic activity
Specific function:
Involved in the catabolism of quinolinic acid (QA).
Gene Name:
QPRT
Uniprot ID:
Q15274
Molecular weight:
30815.28