Phenanthrene
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Basic Info
| Common Name | Phenanthrene(F03455) |
| 2D Structure | |
| Description | Phenanthrene is one of over 100 different polycyclic aromatic hydrocarbons (PAHs). PAHs are chemicals that are formed during the incomplete burning of organic substances, such as fossil fuels. They are usually found as a mixture containing two or more of these compounds. (L10) |
| FRCD ID | F03455 |
| CAS Number | 85-01-8 |
| PubChem CID | 995 |
| Formula | C14H10 |
| IUPAC Name | phenanthrene |
| InChI Key | YNPNZTXNASCQKK-UHFFFAOYSA-N |
| InChI | InChI=1S/C14H10/c1-3-7-13-11(5-1)9-10-12-6-2-4-8-14(12)13/h1-10H |
| Canonical SMILES | C1=CC=C2C(=C1)C=CC3=CC=CC=C32 |
| Isomeric SMILES | C1=CC=C2C(=C1)C=CC3=CC=CC=C32 |
| Wikipedia | Phenanthrene |
| Synonyms |
PHENANTHRENE
Phenanthren [German]
85-01-8
Phenanthren
Phenanthrin
Phenanthracene
Ravatite
Phenantrin
Phenanthrene, pure
UNII-448J8E5BST
|
| Classifies |
Pollutant
|
| Update Date | Nov 13, 2018 17:07 |
Chemical Taxonomy
| Kingdom | Organic compounds |
| Superclass | Benzenoids |
| Class | Phenanthrenes and derivatives |
| Subclass | Not available |
| Intermediate Tree Nodes | Not available |
| Direct Parent | Phenanthrenes and derivatives |
| Alternative Parents | |
| Molecular Framework | Aromatic homopolycyclic compounds |
| Substituents | Phenanthrene - Naphthalene - Aromatic hydrocarbon - Polycyclic hydrocarbon - Unsaturated hydrocarbon - Hydrocarbon - Aromatic homopolycyclic compound |
| Description | This compound belongs to the class of organic compounds known as phenanthrenes and derivatives. These are polycyclic compounds containing a phenanthrene moiety, which is a tricyclic aromatic compound with three non-linearly fused benzene. |
Properties
| Property Name | Property Value |
|---|---|
| Molecular Weight | 178.234 |
| Hydrogen Bond Donor Count | 0 |
| Hydrogen Bond Acceptor Count | 0 |
| Rotatable Bond Count | 0 |
| Complexity | 174 |
| Monoisotopic Mass | 178.078 |
| Exact Mass | 178.078 |
| XLogP | 4.5 |
| Formal Charge | 0 |
| Heavy Atom Count | 14 |
| Defined Atom Stereocenter Count | 0 |
| Undefined Atom Stereocenter Count | 0 |
| Defined Bond Stereocenter Count | 0 |
| Undefined Bond Stereocenter Count | 0 |
| Isotope Atom Count | 0 |
| Covalently-Bonded Unit Count | 1 |
ADMET
| Model | Result | Probability |
|---|---|---|
| Absorption | ||
| Blood-Brain Barrier | BBB+ | 0.9728 |
| Human Intestinal Absorption | HIA+ | 1.0000 |
| Caco-2 Permeability | Caco2+ | 0.8537 |
| P-glycoprotein Substrate | Non-substrate | 0.7437 |
| P-glycoprotein Inhibitor | Non-inhibitor | 0.9276 |
| Non-inhibitor | 0.9361 | |
| Renal Organic Cation Transporter | Non-inhibitor | 0.8178 |
| Distribution | ||
| Subcellular localization | Lysosome | 0.8244 |
| Metabolism | ||
| CYP450 2C9 Substrate | Non-substrate | 0.8091 |
| CYP450 2D6 Substrate | Non-substrate | 0.8874 |
| CYP450 3A4 Substrate | Non-substrate | 0.7722 |
| CYP450 1A2 Inhibitor | Inhibitor | 0.6798 |
| CYP450 2C9 Inhibitor | Non-inhibitor | 0.9070 |
| CYP450 2D6 Inhibitor | Non-inhibitor | 0.9231 |
| CYP450 2C19 Inhibitor | Non-inhibitor | 0.8548 |
| CYP450 3A4 Inhibitor | Non-inhibitor | 0.9288 |
| CYP Inhibitory Promiscuity | High CYP Inhibitory Promiscuity | 0.5335 |
| Excretion | ||
| Toxicity | ||
| Human Ether-a-go-go-Related Gene Inhibition | Weak inhibitor | 0.9317 |
| Non-inhibitor | 0.9054 | |
| AMES Toxicity | AMES toxic | 0.9118 |
| Carcinogens | Non-carcinogens | 0.7059 |
| Fish Toxicity | High FHMT | 0.9391 |
| Tetrahymena Pyriformis Toxicity | High TPT | 0.9959 |
| Honey Bee Toxicity | High HBT | 0.7822 |
| Biodegradation | Not ready biodegradable | 0.8151 |
| Acute Oral Toxicity | III | 0.7913 |
| Carcinogenicity (Three-class) | Warning | 0.4954 |
| Model | Value | Unit |
|---|---|---|
| Absorption | ||
| Aqueous solubility | -6.2526 | LogS |
| Caco-2 Permeability | 1.9501 | LogPapp, cm/s |
| Distribution | ||
| Metabolism | ||
| Excretion | ||
| Toxicity | ||
| Rat Acute Toxicity | 1.9645 | LD50, mol/kg |
| Fish Toxicity | 0.5157 | pLC50, mg/L |
| Tetrahymena Pyriformis Toxicity | 0.9399 | pIGC50, ug/L |
References
| Title | Journal | Date | Pubmed ID |
|---|---|---|---|
| Polycyclic aromatic hydrocarbons in fruits and vegetables: Origin, analysis, and occurrence. | Environ Pollut | 2018 Mar | 29172043 |
| Subcellular distribution and biotransformation of phenanthrene in pakchoi afterinoculation with endophytic Pseudomonas sp. as probed using HRMS coupled withisotope-labeling. | Environ Pollut | 2018 Jun | 29150254 |
| Assessment of addition of biochar to filtering mixtures for potential waterpollutant removal. | Environ Sci Pollut Res Int | 2018 Jan | 29116532 |
| Purification of polluted water with spent mushroom (Agaricus bisporus) substrate:from agricultural waste to biosorbent of phenanthrene, Cd and Pb. | Environ Technol | 2017 Jul | 27776443 |
| Numerical evaluation of bioaccumulation and depuration kinetics of PAHs inMytilus galloprovincialis. | Environ Pollut | 2017 Jan | 27843017 |
| Integrated ecological and chemical food web accumulation modeling explains PAHtemporal trends during regime shifts in a shallow lake. | Water Res | 2017 Aug 1 | 28436825 |
| Proteomic analysis of plasma membrane proteins in wheat roots exposed to phenanthrene. | Environ Sci Pollut Res Int | 2016 Jun | 26897580 |
| Degradation of phenanthrene by Novosphingobium sp. HS2a improved plant growth in PAHs-contaminated environments. | Appl Microbiol Biotechnol | 2016 Dec | 27722914 |
| Comparative proteomic analysis of Arthrobacter phenanthrenivorans Sphe3 onphenanthrene, phthalate and glucose. | J Proteomics | 2015 Jan 15 | 25257624 |
| Zebrafish Abcb4 is a potential efflux transporter of microcystin-LR. | Comp Biochem Physiol C Toxicol Pharmacol | 2015 Jan | 25193616 |
| Diversity of organotrophic bacteria, activity of dehydrogenases and urease as well as seed germination and root growth Lepidium sativum, Sorghum saccharatum and Sinapis alba under the influence of polycyclic aromatic hydrocarbons. | Environ Sci Pollut Res Int | 2015 Dec | 26341339 |
| Influence of feeding and earthworm density on compound bioaccumulation inearthworms Eisenia andrei. | Environ Pollut | 2015 Dec | 26378968 |
| Inoculating plants with the endophytic bacterium Pseudomonas sp. Ph6-gfp toreduce phenanthrene contamination. | Environ Sci Pollut Res Int | 2015 Dec | 26263885 |
| Complete genome sequence of the phenanthrene-degrading soil bacterium Delftiaacidovorans Cs1-4. | Stand Genomic Sci | 2015 Aug 15 | 26380642 |
| Differential degradation of polycyclic aromatic hydrocarbon mixtures byindigenous microbial assemblages in soil. | Lett Appl Microbiol | 2015 Aug | 26031321 |
| Response of uptake and translocation of phenanthrene to nitrogen form in lettuce and wheat seedlings. | Environ Sci Pollut Res Int | 2015 Apr | 25408074 |
| D and E rings may not be indispensable for antofine: discovery of phenanthreneand alkylamine chain containing antofine derivatives as novel antiviral agentsagainst tobacco mosaic virus (TMV) based on interaction of antofine and TMV RNA. | J Agric Food Chem | 2014 Oct 29 | 25154018 |
| Aryl hydrocarbon receptor protein and Cyp1A1 gene induction by LPS and phenanthrene in Atlantic cod (Gadus morhua) head kidney cells. | Fish Shellfish Immunol | 2014 Oct | 25058847 |
| Toxicological effect of single contaminants and contaminant mixtures associatedwith plant ingredients in novel salmon feeds. | Food Chem Toxicol | 2014 Nov | 25193261 |
| Uptake kinetics of five hydrophobic organic pollutants in the earthworm Eisenia fetida in six different soils. | J Hazard Mater | 2014 Feb 28 | 24447858 |
Targets
- 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
- Mechanism of Action:
- 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.
References
- 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 ]
- 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
- Mechanism of Action:
- 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.
References
- 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 ]
- 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
References
- 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 ]
- General Function:
- Zinc ion binding
- Specific Function:
- Nuclear hormone receptor. Binds estrogens with an affinity similar to that of ESR1, and activates expression of reporter genes containing estrogen response elements (ERE) in an estrogen-dependent manner (PubMed:20074560). Isoform beta-cx lacks ligand binding ability and has no or only very low ere binding activity resulting in the loss of ligand-dependent transactivation ability. DNA-binding by ESR1 and ESR2 is rapidly lost at 37 degrees Celsius in the absence of ligand while in the presence of 17 beta-estradiol and 4-hydroxy-tamoxifen loss in DNA-binding at elevated temperature is more gradual.
- Gene Name:
- ESR2
- Uniprot ID:
- Q92731
- Molecular Weight:
- 59215.765 Da
References
- Schmidt JM, Mercure J, Tremblay GB, Page M, Kalbakji A, Feher M, Dunn-Dufault R, Peter MG, Redden PR: De novo design, synthesis, and evaluation of novel nonsteroidal phenanthrene ligands for the estrogen receptor. J Med Chem. 2003 Apr 10;46(8):1408-18. [12672240 ]
- General Function:
- Zinc ion binding
- Specific Function:
- Nuclear hormone receptor. The steroid hormones and their receptors are involved in the regulation of eukaryotic gene expression and affect cellular proliferation and differentiation in target tissues. Ligand-dependent nuclear transactivation involves either direct homodimer binding to a palindromic estrogen response element (ERE) sequence or association with other DNA-binding transcription factors, such as AP-1/c-Jun, c-Fos, ATF-2, Sp1 and Sp3, to mediate ERE-independent signaling. Ligand binding induces a conformational change allowing subsequent or combinatorial association with multiprotein coactivator complexes through LXXLL motifs of their respective components. Mutual transrepression occurs between the estrogen receptor (ER) and NF-kappa-B in a cell-type specific manner. Decreases NF-kappa-B DNA-binding activity and inhibits NF-kappa-B-mediated transcription from the IL6 promoter and displace RELA/p65 and associated coregulators from the promoter. Recruited to the NF-kappa-B response element of the CCL2 and IL8 promoters and can displace CREBBP. Present with NF-kappa-B components RELA/p65 and NFKB1/p50 on ERE sequences. Can also act synergistically with NF-kappa-B to activate transcription involving respective recruitment adjacent response elements; the function involves CREBBP. Can activate the transcriptional activity of TFF1. Also mediates membrane-initiated estrogen signaling involving various kinase cascades. Isoform 3 is involved in activation of NOS3 and endothelial nitric oxide production. Isoforms lacking one or several functional domains are thought to modulate transcriptional activity by competitive ligand or DNA binding and/or heterodimerization with the full length receptor. Essential for MTA1-mediated transcriptional regulation of BRCA1 and BCAS3. Isoform 3 can bind to ERE and inhibit isoform 1.
- Gene Name:
- ESR1
- Uniprot ID:
- P03372
- Molecular Weight:
- 66215.45 Da
References
- Schmidt JM, Mercure J, Tremblay GB, Page M, Kalbakji A, Feher M, Dunn-Dufault R, Peter MG, Redden PR: De novo design, synthesis, and evaluation of novel nonsteroidal phenanthrene ligands for the estrogen receptor. J Med Chem. 2003 Apr 10;46(8):1408-18. [12672240 ]