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Record Information
Version4.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2019-07-23 05:44:36 UTC
HMDB IDHMDB0000926
Secondary Accession Numbers
  • HMDB00926
Metabolite Identification
Common NamePyridine
DescriptionPyridine, also known as py or azabenzene, 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. Pyridine is often used as a denaturant for antifreeze mixtures, for ethyl alcohol, for fungicides, and as a dyeing aid for textiles. In particular, it is known to reduce male fertility and is considered carcinogenic. 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. It is a harmful substance if inhaled, ingested or absorbed through the skin. Pyridine is a very strong basic compound (based on its pKa). Pyridine exists in all living organisms, ranging from bacteria to humans. In humans, pyridine is involved in the metabolic disorder called the nad+ signalling pathway (cancer). Pyridine is an amine, fishy, and putrid tasting compound. Outside of the human body, Pyridine is found, on average, in the highest concentration within kohlrabis and peppermints. Pyridine has also been detected, but not quantified in, several different foods, such as mung beans, celery stalks, tortilla chips, asparagus, and papaya. This could make pyridine a potential biomarker for the consumption of these foods. Pyridine is a clear liquid with an odor that is sour, putrid, and fish-like. Common symptoms of acute exposure to pyridine include: headache, coughing, asthmatic breathing, laryngitis, nausea and vomiting. Pyridine is obtained from crude coal tar or is synthesized from acetaldehyde, formaldehyde and ammonia.
Structure
Data?1563860676
Synonyms
ValueSource
AzabenzeneChEBI
pyChEBI
AzineHMDB
PiridinaHMDB
PirydynaHMDB
PyridinHMDB
TritisanHMDB
Pyridine dinitrateHMDB
Pyridine diphosphateHMDB
Pyridine ion (1-), potassium saltHMDB
Pyridine ion (1-), sodium saltHMDB
Pyridine phosphateHMDB
Pyridine cyanateHMDB
Pyridine hydride (2:1)HMDB
Pyridine hydrochlorideHMDB
Pyridine ion (1-), lithium saltHMDB
Pyridine sulfate (2:1)HMDB
Pyridine, hydrogen bromideHMDB
Pyridine, hydrogen fluorideHMDB
Pyridine, hydrogen iodideHMDB
Pyridine hydrideHMDB
Pyridine ion (2+)HMDB
Pyridine monosulfateHMDB
Pyridine nitrateHMDB
Pyridine phosphate (2:1)HMDB
Pyridine disulfateHMDB
Pyridine ion (1-), hydrogenHMDB
Pyridine monohydrateHMDB
Pyridine monophosphateHMDB
Pyridine perbromate, 82BR-labeledHMDB
Pyridine perchlorateHMDB
Pyridine perchlorate, 2H-labeledHMDB
Pyridine sulfateHMDB
Monopyridine phosphateHMDB
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
Disposition

Route of exposure:

Source:

Biological location:

Role

Environmental role:

Physical Properties
StateLiquid
Experimental Properties
PropertyValueReference
Melting Point-42 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000 mg/mLNot Available
LogP0.65HANSCH,C ET AL. (1995)
Predicted Properties
PropertyValueSource
Water Solubility242 g/LALOGPS
logP0.7ALOGPS
logP0.76ChemAxon
logS0.49ALOGPS
pKa (Strongest Basic)5.12ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area12.89 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity23.9 m³·mol⁻¹ChemAxon
Polarizability8.25 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0ufr-9000000000-445aeb46f419295729deSpectrum
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0fb9-9000000000-f99a956b2e7b0837d371Spectrum
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0ufr-9000000000-8ef2b8f5732d5a1cf292Spectrum
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0ufr-9000000000-b315c8dbb33ca0192ce6Spectrum
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0ufr-9000000000-445aeb46f419295729deSpectrum
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0fb9-9000000000-f99a956b2e7b0837d371Spectrum
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0ufr-9000000000-8ef2b8f5732d5a1cf292Spectrum
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0ufr-9000000000-b315c8dbb33ca0192ce6Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-9000000000-aa03d7534593ae6b2eccSpectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-001i-9000000000-bd7c1ddcf045ad4a0e1bSpectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0f89-9000000000-12fccc7e4109a156a325Spectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0fb9-9000000000-a78e07b9588cf0778962Spectrum
LC-MS/MSLC-MS/MS Spectrum - EI-B (MX-1303) , Positivesplash10-0ufr-9000000000-445aeb46f419295729deSpectrum
LC-MS/MSLC-MS/MS Spectrum - EI-B (Unknown) , Positivesplash10-0fb9-9000000000-f99a956b2e7b0837d371Spectrum
LC-MS/MSLC-MS/MS Spectrum - EI-B (HITACHI RMU-7M) , Positivesplash10-0ufr-9000000000-2cda3d86aa4052c9b258Spectrum
LC-MS/MSLC-MS/MS Spectrum - EI-B (HITACHI M-80B) , Positivesplash10-0ufr-9000000000-f18aef897c61f57d7867Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-001i-9000000000-b74351daa8b967ee139fSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-001i-9000000000-986d33ce2700df9c77c1Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-001i-9000000000-c85235c3074032fc5647Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-001i-9000000000-01968b84d7dd3f9574e3Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-001i-9000200000-e69d6650958a72bb4929Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-001i-9000000000-d87b34d2e067451d9968Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-001i-9000000000-986d33ce2700df9c77c1Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-001i-9000000000-c85235c3074032fc5647Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-001i-9000000000-01968b84d7dd3f9574e3Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-001i-9000200000-e69d6650958a72bb4929Spectrum
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-001i-9000000000-3562137cb32b186627f5Spectrum
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-001i-9000000000-3562137cb32b186627f5Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-9000000000-ab33614a561aa0b36e08Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-9000000000-1fa69045e2c8df7163f9Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-9000000000-ba3853dca7a52b99c4bbSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-9000000000-291f2a9f491fa9ea0f2dSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-681862e3155cf6b42942Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0fb9-9000000000-2b7f3bce495b11121385Spectrum
MSMass Spectrum (Electron Ionization)splash10-0fb9-9000000000-f3974b9899c822b2e9dcSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableSpectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Feces
Tissue Locations
  • Brain
  • Fibroblasts
  • Intestine
  • Kidney
  • Liver
  • Neuron
  • Stratum Corneum
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected but not Quantified Adult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not Quantified Adult (>18 years old)Both
Campylobacter jejuni infection
details
FecesDetected but not Quantified Adult (>18 years old)Both
Clostridium difficile infection
details
FecesDetected but not Quantified Adult (>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
FoodDB IDFDB014733
KNApSAcK IDNot Available
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
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)Download (PDF)
General References
  1. White WB, Yeh SC, Krol GJ: Nitrendipine in human plasma and breast milk. Eur J Clin Pharmacol. 1989;36(5):531-4. [PubMed:2753073 ]
  2. Raemsch KD, Sommer J: Pharmacokinetics and metabolism of nifedipine. Hypertension. 1983 Jul-Aug;5(4 Pt 2):II18-24. [PubMed:6862586 ]
  3. McCormick GT, Sanchez RM: Pyridine extractability of acid-fastness from Mycobacterium leprae. Int J Lepr Other Mycobact Dis. 1979 Sep;47(3):495-9. [PubMed:90667 ]
  4. Wu AH, Bristol B, Sexton K, Cassella-McLane G, Holtman V, Hill DW: Adulteration of urine by "Urine Luck". Clin Chem. 1999 Jul;45(7):1051-7. [PubMed:10388482 ]
  5. Masuoka N, Kodama H, Abe T, Wang DH, Nakano T: Characterization of hydrogen peroxide removal reaction by hemoglobin in the presence of reduced pyridine nucleotides. Biochim Biophys Acta. 2003 Jan 20;1637(1):46-54. [PubMed:12527406 ]
  6. Dru JD, Hsieh JY, Matuszewski BK, Dobrinska MR: Determination of felodipine, its enantiomers, and a pyridine metabolite in human plasma by capillary gas chromatography with mass spectrometric detection. J Chromatogr B Biomed Appl. 1995 Apr 21;666(2):259-67. [PubMed:7633602 ]
  7. Fairbanks LD, Jacomelli G, Micheli V, Slade T, Simmonds HA: Severe pyridine nucleotide depletion in fibroblasts from Lesch-Nyhan patients. Biochem J. 2002 Aug 15;366(Pt 1):265-72. [PubMed:11996669 ]
  8. Sternal RS, Davis MA: In vitro dissolution of cholesterol gallstones. Invest Radiol. 1992 Dec;27(12):1040-3. [PubMed:1473922 ]
  9. Shimada T, Guengerich FP: Activation of amino-alpha-carboline, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine and a copper phthalocyanine cellulose extract of cigarette smoke condensate by cytochrome P-450 enzymes in rat and human liver microsomes. Cancer Res. 1991 Oct 1;51(19):5284-91. [PubMed:1913651 ]
  10. Egorin MJ, Kaplan RS, Salcman M, Aisner J, Colvin M, Wiernik PH, Bachur NR: Cyclophosphamide plasma and cerebrospinal fluid kinetics with and without dimethyl sulfoxide. Clin Pharmacol Ther. 1982 Jul;32(1):122-8. [PubMed:7083726 ]

Enzymes

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