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{{STRUCTURE_4ih5| PDB=4ih5 | SCENE= }}
==Hepatitis C Virus polymerase NS5B (BK) with fragment-based compounds==
===Hepatitis C Virus polymerase NS5B (BK) with fragment-based compounds===
<StructureSection load='4ih5' size='340' side='right' caption='[[4ih5]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
{{ABSTRACT_PUBMED_23509929}}
== Structural highlights ==
<table><tr><td colspan='2'>[[4ih5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Hepatitis_c_virus_(isolate_bk) Hepatitis c virus (isolate bk)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IH5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IH5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=12R:4-(2-PHENYLHYDRAZINYL)-1H-PYRAZOLO[3,4-D]PYRIMIDINE'>12R</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ih6|4ih6]], [[4ih7|4ih7]]</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NS5B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11105 Hepatitis C virus (isolate BK)])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ih5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ih5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ih5 RCSB], [http://www.ebi.ac.uk/pdbsum/4ih5 PDBsum]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The use of fragments with low binding affinity for their targets as starting points has received much attention recently. Screening of fragment libraries has been the most common method to find attractive starting points. Herein, we describe a unique, alternative approach to generating fragment leads. A binding model was developed and a set of guidelines were then selected to use this model to design fragments, enabling our discovery of a novel fragment with high LE.


==Function==
De novo fragment design: a medicinal chemistry approach to fragment-based lead generation.,Talamas FX, Ao-Ieong G, Brameld KA, Chin E, de Vicente J, Dunn JP, Ghate M, Giannetti AM, Harris SF, Labadie SS, Leveque V, Li J, Lui AS, McCaleb KL, Najera I, Schoenfeld RC, Wang B, Wong A J Med Chem. 2013 Apr 11;56(7):3115-9. doi: 10.1021/jm4002605. Epub 2013 Mar 29. PMID:23509929<ref>PMID:23509929</ref>
[[http://www.uniprot.org/uniprot/POLG_HCVBK POLG_HCVBK]] Core protein packages viral RNA to form a viral nucleocapsid, and promotes virion budding. Modulates viral translation initiation by interacting with HCV IRES and 40S ribosomal subunit. Also regulates many host cellular functions such as signaling pathways and apoptosis. Prevents the establishment of cellular antiviral state by blocking the interferon-alpha/beta (IFN-alpha/beta) and IFN-gamma signaling pathways and by inducing human STAT1 degradation. Thought to play a role in virus-mediated cell transformation leading to hepatocellular carcinomas. Interacts with, and activates STAT3 leading to cellular transformation. May repress the promoter of p53, and sequester CREB3 and SP110 isoform 3/Sp110b in the cytoplasm. Also represses cell cycle negative regulating factor CDKN1A, thereby interrupting an important check point of normal cell cycle regulation. Targets transcription factors involved in the regulation of inflammatory responses and in the immune response: suppresses NK-kappaB activation, and activates AP-1. Could mediate apoptotic pathways through association with TNF-type receptors TNFRSF1A and LTBR, although its effect on death receptor-induced apoptosis remains controversial. Enhances TRAIL mediated apoptosis, suggesting that it might play a role in immune-mediated liver cell injury. Seric core protein is able to bind C1QR1 at the T-cell surface, resulting in down-regulation of T-lymphocytes proliferation. May transactivate human MYC, Rous sarcoma virus LTR, and SV40 promoters. May suppress the human FOS and HIV-1 LTR activity. Alters lipid metabolism by interacting with hepatocellular proteins involved in lipid accumulation and storage. Core protein induces up-regulation of FAS promoter activity, and thereby probably contributes to the increased triglyceride accumulation in hepatocytes (steatosis) (By similarity).<ref>PMID:9710605</ref> <ref>PMID:16530520</ref> <ref>PMID:17188392</ref>  E1 and E2 glycoproteins form a heterodimer that is involved in virus attachment to the host cell, virion internalization through clathrin-dependent endocytosis and fusion with host membrane. E1/E2 heterodimer binds to human LDLR, CD81 and SCARB1/SR-BI receptors, but this binding is not sufficient for infection, some additional liver specific cofactors may be needed. The fusion function may possibly be carried by E1. E2 inhibits human EIF2AK2/PKR activation, preventing the establishment of an antiviral state. E2 is a viral ligand for CD209/DC-SIGN and CLEC4M/DC-SIGNR, which are respectively found on dendritic cells (DCs), and on liver sinusoidal endothelial cells and macrophage-like cells of lymph node sinuses. These interactions allow capture of circulating HCV particles by these cells and subsequent transmission to permissive cells. DCs act as sentinels in various tissues where they entrap pathogens and convey them to local lymphoid tissue or lymph node for establishment of immunity. Capture of circulating HCV particles by these SIGN+ cells may facilitate virus infection of proximal hepatocytes and lymphocyte subpopulations and may be essential for the establishment of persistent infection (By similarity).<ref>PMID:9710605</ref> <ref>PMID:16530520</ref> <ref>PMID:17188392</ref>  P7 seems to be a heptameric ion channel protein (viroporin) and is inhibited by the antiviral drug amantadine. Also inhibited by long-alkyl-chain iminosugar derivatives. Essential for infectivity (By similarity).<ref>PMID:9710605</ref> <ref>PMID:16530520</ref> <ref>PMID:17188392</ref>  Protease NS2-3 is a cysteine protease responsible for the autocatalytic cleavage of NS2-NS3. Seems to undergo self-inactivation following maturation (By similarity).<ref>PMID:9710605</ref> <ref>PMID:16530520</ref> <ref>PMID:17188392</ref>  NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS3 serine protease, in association with NS4A, is responsible for the cleavages of NS3-NS4A, NS4A-NS4B, NS4B-NS5A and NS5A-NS5B. NS3/NS4A complex also prevents phosphorylation of human IRF3, thus preventing the establishment of dsRNA induced antiviral state. NS3 RNA helicase binds to RNA and unwinds dsRNA in the 3' to 5' direction, and likely RNA stable secondary structure in the template strand. Cleaves and inhibits the host antiviral protein MAVS (By similarity).<ref>PMID:9710605</ref> <ref>PMID:16530520</ref> <ref>PMID:17188392</ref>  NS4B induces a specific membrane alteration that serves as a scaffold for the virus replication complex. This membrane alteration gives rise to the so-called ER-derived membranous web that contains the replication complex (By similarity).<ref>PMID:9710605</ref> <ref>PMID:16530520</ref> <ref>PMID:17188392</ref>  NS5A is a component of the replication complex involved in RNA-binding. Its interaction with Human VAPB may target the viral replication complex to vesicles. Down-regulates viral IRES translation initiation. Mediates interferon resistance, presumably by interacting with and inhibiting human EIF2AK2/PKR. Seems to inhibit apoptosis by interacting with BIN1 and FKBP8. The hyperphosphorylated form of NS5A is an inhibitor of viral replication (By similarity).<ref>PMID:9710605</ref> <ref>PMID:16530520</ref> <ref>PMID:17188392</ref>  NS5B is a RNA-dependent RNA polymerase that plays an essential role in the virus replication (By similarity).<ref>PMID:9710605</ref> <ref>PMID:16530520</ref> <ref>PMID:17188392</ref>


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[4ih5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Hepatitis_c_virus_(isolate_bk) Hepatitis c virus (isolate bk)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IH5 OCA].
</div>


==Reference==
==See Also==
<ref group="xtra">PMID:023509929</ref><references group="xtra"/><references/>
*[[RNA polymerase|RNA polymerase]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: RNA-directed RNA polymerase]]
[[Category: RNA-directed RNA polymerase]]
[[Category: Ghate, M.]]
[[Category: Ghate, M]]
[[Category: Harris, S F.]]
[[Category: Harris, S F]]
[[Category: Fragment based drug design]]
[[Category: Fragment based drug design]]
[[Category: Transferase-transferase inhibitor complex]]
[[Category: Transferase-transferase inhibitor complex]]

Revision as of 15:43, 21 December 2014

Hepatitis C Virus polymerase NS5B (BK) with fragment-based compoundsHepatitis C Virus polymerase NS5B (BK) with fragment-based compounds

Structural highlights

4ih5 is a 2 chain structure with sequence from Hepatitis c virus (isolate bk). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:NS5B (Hepatitis C virus (isolate BK))
Activity:RNA-directed RNA polymerase, with EC number 2.7.7.48
Resources:FirstGlance, OCA, RCSB, PDBsum

Publication Abstract from PubMed

The use of fragments with low binding affinity for their targets as starting points has received much attention recently. Screening of fragment libraries has been the most common method to find attractive starting points. Herein, we describe a unique, alternative approach to generating fragment leads. A binding model was developed and a set of guidelines were then selected to use this model to design fragments, enabling our discovery of a novel fragment with high LE.

De novo fragment design: a medicinal chemistry approach to fragment-based lead generation.,Talamas FX, Ao-Ieong G, Brameld KA, Chin E, de Vicente J, Dunn JP, Ghate M, Giannetti AM, Harris SF, Labadie SS, Leveque V, Li J, Lui AS, McCaleb KL, Najera I, Schoenfeld RC, Wang B, Wong A J Med Chem. 2013 Apr 11;56(7):3115-9. doi: 10.1021/jm4002605. Epub 2013 Mar 29. PMID:23509929[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Talamas FX, Ao-Ieong G, Brameld KA, Chin E, de Vicente J, Dunn JP, Ghate M, Giannetti AM, Harris SF, Labadie SS, Leveque V, Li J, Lui AS, McCaleb KL, Najera I, Schoenfeld RC, Wang B, Wong A. De novo fragment design: a medicinal chemistry approach to fragment-based lead generation. J Med Chem. 2013 Apr 11;56(7):3115-9. doi: 10.1021/jm4002605. Epub 2013 Mar 29. PMID:23509929 doi:10.1021/jm4002605

4ih5, resolution 1.90Å

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