You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2016-02-11 01:03:34 UTC
HMDB IDHMDB00926
Secondary Accession NumbersNone
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
Thumb
Synonyms
ValueSource
AzabenzeneChEBI
pyChEBI
AzineHMDB
PiridinaHMDB
PirydynaHMDB
PyridinHMDB
TritisanHMDB
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 KeyInChIKey=JUJWROOIHBZHMG-UHFFFAOYSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as pyridines and derivatives. These 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
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
StatusDetected but not Quantified
Origin
  • Toxin/Pollutant
BiofunctionNot Available
ApplicationNot Available
Cellular locationsNot Available
Physical Properties
StateLiquid
Experimental Properties
PropertyValueReference
Melting Point-42 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000.0 mg/mLNot Available
LogP0.65HANSCH,C ET AL. (1995)
Predicted Properties
PropertyValueSource
Water Solubility242.0 mg/mLALOGPS
logP0.7ALOGPS
logP0.76ChemAxon
logS0.49ALOGPS
pKa (Strongest Basic)5.12ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area12.89 Å2ChemAxon
Rotatable Bond Count0ChemAxon
Refractivity23.9 m3·mol-1ChemAxon
Polarizability8.25 Å3ChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-001i-9000000000-bd7c1ddcf045ad4a0e1bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0f89-9000000000-12fccc7e4109a156a325View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0fb9-9000000000-a78e07b9588cf0778962View in MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (MX-1303) , Positivesplash10-0ufr-9000000000-445aeb46f419295729deView in MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (Unknown) , Positivesplash10-0fb9-9000000000-f99a956b2e7b0837d371View in MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (HITACHI RMU-7M) , Positivesplash10-0ufr-9000000000-2cda3d86aa4052c9b258View in MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (HITACHI M-80B) , Positivesplash10-0ufr-9000000000-f18aef897c61f57d7867View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-001i-9000000000-b74351daa8b967ee139fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-001i-9000000000-986d33ce2700df9c77c1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-001i-9000000000-c85235c3074032fc5647View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-001i-9000000000-01968b84d7dd3f9574e3View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-001i-9000200000-e69d6650958a72bb4929View in MoNA
MSMass Spectrum (Electron Ionization)splash10-0fb9-9000000000-f3974b9899c822b2e9dcView in MoNA
1D NMR13C NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR13C NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
Biological Properties
Cellular LocationsNot Available
Biofluid Locations
  • Feces
Tissue Location
  • Brain
  • Fibroblasts
  • Intestine
  • Kidney
  • Liver
  • Neuron
  • Stratum Corneum
PathwaysNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot ApplicableAdult (>18 years old)Both
Normal
details
FecesDetected but not QuantifiedNot ApplicableAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot ApplicableAdult (>18 years old)Both
Campylobacter jejuni infection
details
FecesDetected but not QuantifiedNot ApplicableAdult (>18 years old)Both
Clostridium difficile infection
details
FecesDetected but not QuantifiedNot ApplicableAdult (>18 years old)Both
Ulcerative Colitis
details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB014733
KNApSAcK IDNot Available
Chemspider ID1020
KEGG Compound IDC00747
BioCyc IDPYRIDINE-RING
BiGG IDNot Available
Wikipedia LinkPyridine
NuGOwiki LinkHMDB00926
Metagene LinkHMDB00926
METLIN ID5877
PubChem Compound1049
PDB ID0PY
ChEBI ID16227
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. [2753073 ]
  2. Raemsch KD, Sommer J: Pharmacokinetics and metabolism of nifedipine. Hypertension. 1983 Jul-Aug;5(4 Pt 2):II18-24. [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. [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. [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. [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. [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. [11996669 ]
  8. Sternal RS, Davis MA: In vitro dissolution of cholesterol gallstones. Invest Radiol. 1992 Dec;27(12):1040-3. [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. [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. [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