Pyrene (T3D0253)

IdentificationTaxonomyBiological PropertiesPhysical PropertiesToxicity ProfileSpectraConcentrationsLinksReferencesGene RegulationTargets (8)XML
Targets (8)
Record Information
Version2.0
Creation Date2009-03-06 18:58:22 UTC
Update Date2014-12-24 20:21:25 UTC
Accession NumberT3D0253
Identification
Common NamePyrene
ClassSmall Molecule
DescriptionPyrene is a polycyclic aromatic hydrocarbon (PAH) consisting of four fused benzene rings, resulting in a flat aromatic system. The chemical formula is C16H10. This colourless solid is the smallest peri-fused PAH (one where the rings are fused through more than one face). Pyrene forms during incomplete combustion of organic compounds. Although it is not as problematic as benzopyrene, animal studies have shown pyrene is toxic to the kidneys and the liver.
Compound Type
  • Aromatic Hydrocarbon
  • Food Toxin
  • Industrial By-product/Pollutant
  • Industrial/Workplace Toxin
  • Metabolite
  • Natural Compound
  • Organic Compound
  • Pollutant
  • Polycyclic Aromatic Hydrocarbon
Chemical Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
Synonym
Benzo[def]phenanthrene
Benzpyrene
beta-Pyrene
{Benzo[def]phenanthrene}
Chemical FormulaC16H10
Average Molecular Mass202.251 g/mol
Monoisotopic Mass202.078 g/mol
CAS Registry Number129-00-0
IUPAC Namepyrene
Traditional Namepyrene
SMILESC1=CC2=C3C(C=CC4=CC=CC(C=C2)=C34)=C1
InChI IdentifierInChI=1S/C16H10/c1-3-11-7-9-13-5-2-6-14-10-8-12(4-1)15(11)16(13)14/h1-10H
InChI KeyInChIKey=BBEAQIROQSPTKN-UHFFFAOYSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyrenes. Pyrenes are compounds containing a pyrene moiety, which consists four fused benzene rings, resulting in a flat aromatic system.
KingdomOrganic compounds
Super ClassBenzenoids
ClassPyrenes
Sub ClassNot Available
Direct ParentPyrenes
Alternative Parents
Substituents
  • Pyrene
  • Phenanthrene
  • Naphthalene
  • Aromatic hydrocarbon
  • Polycyclic hydrocarbon
  • Unsaturated hydrocarbon
  • Hydrocarbon
  • Aromatic homopolycyclic compound
Molecular FrameworkAromatic homopolycyclic compounds
External Descriptors
Biological Properties
StatusDetected and Not Quantified
OriginExogenous
Cellular Locations
  • Membrane
Biofluid LocationsNot Available
Tissue LocationsNot Available
PathwaysNot Available
ApplicationsNot Available
Biological RolesNot Available
Chemical RolesNot Available
Physical Properties
StateSolid
AppearanceColorless solid.
Experimental Properties
PropertyValue
Melting Point151.2°C
Boiling Point404°C (759.2°F)
Solubility0.000135 mg/mL at 25°C
LogP4.88
Predicted Properties
PropertyValueSource
Water Solubility2.3e-05 g/LALOGPS
logP5.19ALOGPS
logP4.28ChemAxon
logS-6.9ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity66.72 m³·mol⁻¹ChemAxon
Polarizability22.86 ųChemAxon
Number of Rings4ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateView
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0udi-3490000000-a0f4fc47f1f625d9dda52017-09-12View Spectrum
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0udi-0390000000-aed9be9c54a99a10a7722017-09-12View Spectrum
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0udi-0190000000-ab79745741c952b34e152017-09-12View Spectrum
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0udi-1290000000-1f9a049804cf2fb46ba32017-09-12View Spectrum
GC-MSGC-MS Spectrum - CI-B (Non-derivatized)splash10-0udi-0090000000-838134ca9d5c1b6a304a2017-09-12View Spectrum
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0udi-3490000000-a0f4fc47f1f625d9dda52018-05-18View Spectrum
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0udi-0390000000-aed9be9c54a99a10a7722018-05-18View Spectrum
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0udi-0190000000-ab79745741c952b34e152018-05-18View Spectrum
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0udi-1290000000-1f9a049804cf2fb46ba32018-05-18View Spectrum
GC-MSGC-MS Spectrum - CI-B (Non-derivatized)splash10-0udi-0090000000-838134ca9d5c1b6a304a2018-05-18View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0udi-0090000000-023bdea6eb26657bf7c22017-09-01View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0090000000-8a4ffb969c6480f4a0f92016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0090000000-8a4ffb969c6480f4a0f92016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-0190000000-cf9d9c3c3318712878832016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-0090000000-e5a45f3b87aa2e8b24042016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0udi-0090000000-e5a45f3b87aa2e8b24042016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0udi-0090000000-650c1cb3eed690571b3a2016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-0090000000-6aba671a40209155866b2021-09-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0udi-0090000000-6aba671a40209155866b2021-09-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0udi-0090000000-6aba671a40209155866b2021-09-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0090000000-d631c56cd3c088dbebc42021-09-25View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0090000000-d631c56cd3c088dbebc42021-09-25View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-0090000000-37848fb7edb6a1e2deda2021-09-25View Spectrum
MSMass Spectrum (Electron Ionization)splash10-0udi-0190000000-3f6dbb289af8f6c988fb2014-09-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, CDCl3, experimental)Not Available2014-09-20View Spectrum
1D NMR13C NMR Spectrum (1D, 25.16 MHz, CDCl3, experimental)Not Available2014-09-23View Spectrum
Toxicity Profile
Route of ExposureOral (4) ; inhalation (4)
Mechanism of ToxicityThe ability of PAH's to bind to blood proteins such as albumin allows them to be transported throughout the body. Many PAH's induce the expression of cytochrome P450 enzymes, especially CYP1A1, CYP1A2, and CYP1B1, by binding to the aryl hydrocarbon receptor or glycine N-methyltransferase protein. These enzymes metabolize PAH's into their toxic intermediates. The reactive metabolites of PAHs (epoxide intermediates, dihydrodiols, phenols, quinones, and their various combinations) covalently bind to DNA and other cellular macromolecules, initiating mutagenesis and carcinogenesis. (4, 5, 2, 3)
MetabolismPAH metabolism occurs in all tissues, usually by cytochrome P-450 and its associated enzymes. PAHs are metabolized into reactive intermediates, which include epoxide intermediates, dihydrodiols, phenols, quinones, and their various combinations. The phenols, quinones, and dihydrodiols can all be conjugated to glucuronides and sulfate esters; the quinones also form glutathione conjugates. (4)
Toxicity ValuesLD50: 2700 mg/kg (Oral, Rat) (7)
Lethal DoseNot Available
Carcinogenicity (IARC Classification)3, not classifiable as to its carcinogenicity to humans. (6)
Uses/SourcesPAHs are released into the environment via the combustion of fossil fuels, coke oven emissions and vehicle exhausts, as well as naturally from forest fires and vocanic eruptions. PAHs from these sources may contaminate nearly water systems. They are also found in coal tar and charbroiled food. (4)
Minimum Risk LevelNot Available
Health EffectsPAHs are carcinogens and have been associated with the increased risk of skin, respiratory tract, bladder, stomach, and kidney cancers. They may also cause reproductive effects and depress the immune system. (4)
SymptomsAcute exposure to PAHs causes irritation and inflammation of the skin and lung tissue. (1)
TreatmentThere is no know antidote for PAHs. Exposure is usually handled with symptomatic treatment. (4)
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
DrugBank IDNot Available
HMDB IDHMDB42002
PubChem Compound ID31423
ChEMBL IDCHEMBL279564
ChemSpider ID29153
KEGG IDC14335
UniProt IDNot Available
OMIM ID
ChEBI ID39106
BioCyc IDNot Available
CTD IDNot Available
Stitch IDPyrene
PDB IDNot Available
ACToR IDNot Available
Wikipedia LinkPyrene
References
Synthesis ReferenceNot Available
MSDSLink
General References
  1. Santodonato J, Howard P, Basu D: Health and ecological assessment of polynuclear aromatic hydrocarbons. J Environ Pathol Toxicol. 1981 Sep;5(1):1-364. [7310260 ]
  2. Uno S, Dragin N, Miller ML, Dalton TP, Gonzalez FJ, Nebert DW: Basal and inducible CYP1 mRNA quantitation and protein localization throughout the mouse gastrointestinal tract. Free Radic Biol Med. 2008 Feb 15;44(4):570-83. Epub 2007 Nov 12. [17997381 ]
  3. Padros J, Pelletier E: In vivo formation of (+)-anti-benzo[a]pyrene diol-epoxide-plasma albumin adducts in fish. Mar Environ Res. 2000 Jul-Dec;50(1-5):347-51. [11460716 ]
  4. ATSDR - Agency for Toxic Substances and Disease Registry (1995). Toxicological profile for PAHs. U.S. Public Health Service in collaboration with U.S. Environmental Protection Agency (EPA). [Link]
  5. Wikipedia. Benzopyrene. Last Updated 22 January 2009. [Link]
  6. International Agency for Research on Cancer (2014). IARC Monographs on the Evaluation of Carcinogenic Risks to Humans. [Link]
  7. The Physical and Theoretical Chemistry Laboratory of Oxford University (2004). Material Safety Data Sheet (MSDS) for pyrene. [Link]
Gene Regulation
Up-Regulated Genes
GeneGene SymbolGene IDInteractionChromosomeDetails
Down-Regulated GenesNot Available

Targets

Target Details
1. Aryl hydrocarbon receptor
General Function:
Transcription regulatory region dna binding
Specific Function:
Ligand-activated transcriptional activator. Binds to the XRE promoter region of genes it activates. Activates the expression of multiple phase I and II xenobiotic chemical metabolizing enzyme genes (such as the CYP1A1 gene). Mediates biochemical and toxic effects of halogenated aromatic hydrocarbons. Involved in cell-cycle regulation. Likely to play an important role in the development and maturation of many tissues. Regulates the circadian clock by inhibiting the basal and circadian expression of the core circadian component PER1. Inhibits PER1 by repressing the CLOCK-ARNTL/BMAL1 heterodimer mediated transcriptional activation of PER1.
Gene Name:
AHR
Uniprot ID:
P35869
Molecular Weight:
96146.705 Da
References
  1. Uno S, Dragin N, Miller ML, Dalton TP, Gonzalez FJ, Nebert DW: Basal and inducible CYP1 mRNA quantitation and protein localization throughout the mouse gastrointestinal tract. Free Radic Biol Med. 2008 Feb 15;44(4):570-83. Epub 2007 Nov 12. [17997381 ]
  2. Padros J, Pelletier E: In vivo formation of (+)-anti-benzo[a]pyrene diol-epoxide-plasma albumin adducts in fish. Mar Environ Res. 2000 Jul-Dec;50(1-5):347-51. [11460716 ]
  3. ATSDR - Agency for Toxic Substances and Disease Registry (1995). Toxicological profile for PAHs. U.S. Public Health Service in collaboration with U.S. Environmental Protection Agency (EPA). [Link]
  4. Wikipedia. Benzopyrene. Last Updated 22 January 2009. [Link]
2. DNA
General Function:
Used for biological information storage.
Specific Function:
DNA contains the instructions needed for an organism to develop, survive and reproduce.
Molecular Weight:
2.15 x 1012 Da
References
  1. Uno S, Dragin N, Miller ML, Dalton TP, Gonzalez FJ, Nebert DW: Basal and inducible CYP1 mRNA quantitation and protein localization throughout the mouse gastrointestinal tract. Free Radic Biol Med. 2008 Feb 15;44(4):570-83. Epub 2007 Nov 12. [17997381 ]
  2. Padros J, Pelletier E: In vivo formation of (+)-anti-benzo[a]pyrene diol-epoxide-plasma albumin adducts in fish. Mar Environ Res. 2000 Jul-Dec;50(1-5):347-51. [11460716 ]
  3. ATSDR - Agency for Toxic Substances and Disease Registry (1995). Toxicological profile for PAHs. U.S. Public Health Service in collaboration with U.S. Environmental Protection Agency (EPA). [Link]
  4. Wikipedia. Benzopyrene. Last Updated 22 January 2009. [Link]
Target Details
3. Glycine N-methyltransferase
General Function:
Glycine n-methyltransferase activity
Specific Function:
Catalyzes the methylation of glycine by using S-adenosylmethionine (AdoMet) to form N-methylglycine (sarcosine) with the concomitant production of S-adenosylhomocysteine (AdoHcy). Possible crucial role in the regulation of tissue concentration of AdoMet and of metabolism of methionine.
Gene Name:
GNMT
Uniprot ID:
Q14749
Molecular Weight:
32742.0 Da
References
  1. Uno S, Dragin N, Miller ML, Dalton TP, Gonzalez FJ, Nebert DW: Basal and inducible CYP1 mRNA quantitation and protein localization throughout the mouse gastrointestinal tract. Free Radic Biol Med. 2008 Feb 15;44(4):570-83. Epub 2007 Nov 12. [17997381 ]
  2. Padros J, Pelletier E: In vivo formation of (+)-anti-benzo[a]pyrene diol-epoxide-plasma albumin adducts in fish. Mar Environ Res. 2000 Jul-Dec;50(1-5):347-51. [11460716 ]
  3. ATSDR - Agency for Toxic Substances and Disease Registry (1995). Toxicological profile for PAHs. U.S. Public Health Service in collaboration with U.S. Environmental Protection Agency (EPA). [Link]
  4. Wikipedia. Benzopyrene. Last Updated 22 January 2009. [Link]
Target Details
4. Cytochrome P450 1B1
General Function:
Oxygen binding
Specific Function:
Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, retinoid and xenobiotics. Preferentially oxidizes 17beta-estradiol to the carcinogenic 4-hydroxy derivative, and a variety of procarcinogenic compounds to their activated forms, including polycyclic aromatic hydrocarbons. Promotes angiogenesis by removing cellular oxygenation products, thereby decreasing oxidative stress, release of antiangiogenic factor THBS2, then allowing endothelial cells migration, cell adhesion and capillary morphogenesis. These changes are concommitant with the endothelial nitric oxide synthase activity and nitric oxide synthesis. Plays an important role in the regulation of perivascular cell proliferation, migration, and survival through modulation of the intracellular oxidative state and NF-kappa-B expression and/or activity, during angiogenesis. Contributes to oxidative homeostasis and ultrastructural organization and function of trabecular meshwork tissue through modulation of POSTN expression.
Gene Name:
CYP1B1
Uniprot ID:
Q16678
Molecular Weight:
60845.33 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
IC500.002 uMNot AvailableBindingDB 50214608
References
  1. Bruno RD, Njar VC: Targeting cytochrome P450 enzymes: a new approach in anti-cancer drug development. Bioorg Med Chem. 2007 Aug 1;15(15):5047-60. Epub 2007 May 23. [17544277 ]
  2. Shimada T, Tanaka K, Takenaka S, Foroozesh MK, Murayama N, Yamazaki H, Guengerich FP, Komori M: Reverse type I binding spectra of human cytochrome P450 1B1 induced by flavonoid, stilbene, pyrene, naphthalene, phenanthrene, and biphenyl derivatives that inhibit catalytic activity: a structure-function relationship study. Chem Res Toxicol. 2009 Jul;22(7):1325-33. doi: 10.1021/tx900127s. [19563207 ]
Target Details
5. Cytochrome P450 1A1
General Function:
Vitamin d 24-hydroxylase activity
Specific Function:
Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.
Gene Name:
CYP1A1
Uniprot ID:
P04798
Molecular Weight:
58164.815 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
IC500.041 uMNot AvailableBindingDB 50214608
References
  1. Bruno RD, Njar VC: Targeting cytochrome P450 enzymes: a new approach in anti-cancer drug development. Bioorg Med Chem. 2007 Aug 1;15(15):5047-60. Epub 2007 May 23. [17544277 ]
Target Details
6. Cytochrome P450 1A2
General Function:
Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
Specific Function:
Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Most active in catalyzing 2-hydroxylation. Caffeine is metabolized primarily by cytochrome CYP1A2 in the liver through an initial N3-demethylation. Also acts in the metabolism of aflatoxin B1 and acetaminophen. Participates in the bioactivation of carcinogenic aromatic and heterocyclic amines. Catalizes the N-hydroxylation of heterocyclic amines and the O-deethylation of phenacetin.
Gene Name:
CYP1A2
Uniprot ID:
P05177
Molecular Weight:
58293.76 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
IC500.007 uMNot AvailableBindingDB 50214608
References
  1. Bruno RD, Njar VC: Targeting cytochrome P450 enzymes: a new approach in anti-cancer drug development. Bioorg Med Chem. 2007 Aug 1;15(15):5047-60. Epub 2007 May 23. [17544277 ]
Target Details
7. Nuclear receptor subfamily 1 group I member 3
General Function:
Zinc ion binding
Specific Function:
Binds and transactivates the retinoic acid response elements that control expression of the retinoic acid receptor beta 2 and alcohol dehydrogenase 3 genes. Transactivates both the phenobarbital responsive element module of the human CYP2B6 gene and the CYP3A4 xenobiotic response element.
Gene Name:
NR1I3
Uniprot ID:
Q14994
Molecular Weight:
39942.145 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
AC501.49 uMATG_CAR_TRANSAttagene
References
  1. Sipes NS, Martin MT, Kothiya P, Reif DM, Judson RS, Richard AM, Houck KA, Dix DJ, Kavlock RJ, Knudsen TB: Profiling 976 ToxCast chemicals across 331 enzymatic and receptor signaling assays. Chem Res Toxicol. 2013 Jun 17;26(6):878-95. doi: 10.1021/tx400021f. Epub 2013 May 16. [23611293 ]
Target Details
8. Nuclear receptor subfamily 1 group I member 2
General Function:
Zinc ion binding
Specific Function:
Nuclear receptor that binds and is activated by variety of endogenous and xenobiotic compounds. Transcription factor that activates the transcription of multiple genes involved in the metabolism and secretion of potentially harmful xenobiotics, drugs and endogenous compounds. Activated by the antibiotic rifampicin and various plant metabolites, such as hyperforin, guggulipid, colupulone, and isoflavones. Response to specific ligands is species-specific. Activated by naturally occurring steroids, such as pregnenolone and progesterone. Binds to a response element in the promoters of the CYP3A4 and ABCB1/MDR1 genes.
Gene Name:
NR1I2
Uniprot ID:
O75469
Molecular Weight:
49761.245 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
AC505.62 uMATG_PXR_TRANSAttagene
AC509.77 uMATG_PXRE_CISAttagene
References
  1. Sipes NS, Martin MT, Kothiya P, Reif DM, Judson RS, Richard AM, Houck KA, Dix DJ, Kavlock RJ, Knudsen TB: Profiling 976 ToxCast chemicals across 331 enzymatic and receptor signaling assays. Chem Res Toxicol. 2013 Jun 17;26(6):878-95. doi: 10.1021/tx400021f. Epub 2013 May 16. [23611293 ]