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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-10-13 04:31:51 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
Data?1582752165
Synonyms
ValueSource
AzabenzeneChEBI
pyChEBI
AzineHMDB
PiridinaHMDB
PirydynaHMDB
PyridinHMDB
TritisanHMDB
Pyridine dinitrateMeSH, HMDB
Pyridine diphosphateMeSH, HMDB
Pyridine ion (1-), potassium saltMeSH, HMDB
Pyridine ion (1-), sodium saltMeSH, HMDB
Pyridine phosphateMeSH, HMDB
Pyridine cyanateMeSH, HMDB
Pyridine hydride (2:1)MeSH, HMDB
Pyridine hydrochlorideMeSH, HMDB
Pyridine ion (1-), lithium saltMeSH, HMDB
Pyridine sulfate (2:1)MeSH, HMDB
Pyridine, hydrogen bromideMeSH, HMDB
Pyridine, hydrogen fluorideMeSH, HMDB
Pyridine, hydrogen iodideMeSH, HMDB
Pyridine hydrideMeSH, HMDB
Pyridine ion (2+)MeSH, HMDB
Pyridine monosulfateMeSH, HMDB
Pyridine nitrateMeSH, HMDB
Pyridine phosphate (2:1)MeSH, HMDB
Pyridine disulfateMeSH, HMDB
Pyridine ion (1-), hydrogenMeSH, HMDB
Pyridine monohydrateMeSH, HMDB
Pyridine monophosphateMeSH, HMDB
Pyridine perbromate, 82BR-labeledMeSH, HMDB
Pyridine perchlorateMeSH, HMDB
Pyridine perchlorate, 2H-labeledMeSH, HMDB
Pyridine sulfateMeSH, HMDB
Monopyridine phosphateMeSH, HMDB
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

Biological location

Source

Route of exposure

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 Spectral PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility242 g/LALOGPS
logP10(0.7) g/LALOGPS
logP10(0.76) g/LChemAxon
logS10(0.49) g/LALOGPS
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
Predicted Spectral Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+110.78931661259
DarkChem[M-H]-105.81131661259
AllCCS[M+H]+113.59632859911
AllCCS[M-H]-115.4432859911

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - Pyridine EI-B (Non-derivatized)splash10-0ufr-9000000000-445aeb46f419295729de2017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Pyridine EI-B (Non-derivatized)splash10-0fb9-9000000000-f99a956b2e7b0837d3712017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Pyridine EI-B (Non-derivatized)splash10-0ufr-9000000000-8ef2b8f5732d5a1cf2922017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Pyridine EI-B (Non-derivatized)splash10-0ufr-9000000000-b315c8dbb33ca0192ce62017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Pyridine EI-B (Non-derivatized)splash10-0ufr-9000000000-445aeb46f419295729de2018-05-18HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Pyridine EI-B (Non-derivatized)splash10-0fb9-9000000000-f99a956b2e7b0837d3712018-05-18HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Pyridine EI-B (Non-derivatized)splash10-0ufr-9000000000-8ef2b8f5732d5a1cf2922018-05-18HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Pyridine EI-B (Non-derivatized)splash10-0ufr-9000000000-b315c8dbb33ca0192ce62018-05-18HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pyridine GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-9000000000-aa03d7534593ae6b2ecc2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pyridine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
MSMass Spectrum (Electron Ionization)splash10-0fb9-9000000000-f3974b9899c822b2e9dc2015-03-01Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine Quattro_QQQ 10V, Positive-QTOF (Annotated)splash10-001i-9000000000-bd7c1ddcf045ad4a0e1b2012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine Quattro_QQQ 25V, Positive-QTOF (Annotated)splash10-0f89-9000000000-12fccc7e4109a156a3252012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine Quattro_QQQ 40V, Positive-QTOF (Annotated)splash10-0fb9-9000000000-a78e07b9588cf07789622012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine EI-B (MX-1303) , Positive-QTOFsplash10-0ufr-9000000000-445aeb46f419295729de2012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine EI-B (Unknown) , Positive-QTOFsplash10-0fb9-9000000000-f99a956b2e7b0837d3712012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine EI-B (HITACHI RMU-7M) , Positive-QTOFsplash10-0ufr-9000000000-2cda3d86aa4052c9b2582012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine EI-B (HITACHI M-80B) , Positive-QTOFsplash10-0ufr-9000000000-f18aef897c61f57d78672012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive-QTOFsplash10-001i-9000000000-b74351daa8b967ee139f2012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive-QTOFsplash10-001i-9000000000-986d33ce2700df9c77c12012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive-QTOFsplash10-001i-9000000000-c85235c3074032fc56472012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive-QTOFsplash10-001i-9000000000-01968b84d7dd3f9574e32012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive-QTOFsplash10-001i-9000200000-e69d6650958a72bb49292012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine LC-ESI-QQ , positive-QTOFsplash10-001i-9000000000-d87b34d2e067451d99682017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine LC-ESI-QQ , positive-QTOFsplash10-001i-9000000000-986d33ce2700df9c77c12017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine LC-ESI-QQ , positive-QTOFsplash10-001i-9000000000-c85235c3074032fc56472017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine LC-ESI-QQ , positive-QTOFsplash10-001i-9000000000-01968b84d7dd3f9574e32017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine LC-ESI-QQ , positive-QTOFsplash10-001i-9000200000-e69d6650958a72bb49292017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine ESI-ITFT , positive-QTOFsplash10-001i-9000000000-3562137cb32b186627f52017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Pyridine ESI-ITFT , positive-QTOFsplash10-001i-9000000000-3562137cb32b186627f52017-09-14HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyridine 10V, Positive-QTOFsplash10-001i-9000000000-ab33614a561aa0b36e082017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyridine 20V, Positive-QTOFsplash10-001i-9000000000-1fa69045e2c8df7163f92017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyridine 40V, Positive-QTOFsplash10-0udi-9000000000-ba3853dca7a52b99c4bb2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyridine 10V, Negative-QTOFsplash10-004i-9000000000-291f2a9f491fa9ea0f2d2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyridine 20V, Negative-QTOFsplash10-004i-9000000000-681862e3155cf6b429422017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pyridine 40V, Negative-QTOFsplash10-0fb9-9000000000-2b7f3bce495b111213852017-09-01Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)2012-12-05Wishart LabView Spectrum
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)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