1NHV

Hepatitis C virus RNA polymerase in complex with non-nucleoside analogue inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.251 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Non-Nucleoside Analogue Inhibitors Bind to an Allosteric Site on HCV NS5B Polymerase: Crystal Structures and Mechanism of Inhibition

Wang, M.Ng, K.K.S.Cherney, M.M.Chan, L.Yannopoulos, C.G.Bedard, J.Morin, N.Nguyen-Ba, N.Alaoui-Ismaili, M.H.Bethell, R.C.James, M.N.G.

(2003) J Biol Chem 278: 9489-9495

  • DOI: 10.1074/jbc.M209397200
  • Primary Citation of Related Structures:  
    1NHU, 1NHV

  • PubMed Abstract: 
  • X-ray crystal structures of two non-nucleoside analogue inhibitors bound to hepatitis C virus NS5B RNA-dependent RNA polymerase have been determined to 2.0 and 2.9 A resolution. These noncompetitive inhibitors bind to the same site on the protein, approximately 35 A from the active site ...

    X-ray crystal structures of two non-nucleoside analogue inhibitors bound to hepatitis C virus NS5B RNA-dependent RNA polymerase have been determined to 2.0 and 2.9 A resolution. These noncompetitive inhibitors bind to the same site on the protein, approximately 35 A from the active site. The common features of binding include a large hydrophobic region and two hydrogen bonds between both oxygen atoms of a carboxylate group on the inhibitor and two main chain amide nitrogen atoms of Ser(476) and Tyr(477) on NS5B. The inhibitor-binding site lies at the base of the thumb domain, near its interface with the C-terminal extension of NS5B. The location of this inhibitor-binding site suggests that the binding of these inhibitors interferes with a conformational change essential for the activity of the polymerase.


    Organizational Affiliation

    Canadian Institutes for Health Research Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASEA, B578Hepatitis C virus subtype 1bMutation(s): 0 
EC: 2.7.7.48 (PDB Primary Data), 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
UniProt
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK))
Explore P26663 
Go to UniProtKB:  P26663
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
154 (Subject of Investigation/LOI)
Query on 154

Download Ideal Coordinates CCD File 
C [auth A], D [auth B](2S)-2-[(5-BENZOFURAN-2-YL-THIOPHEN-2-YLMETHYL)-(2,4-DICHLORO-BENZOYL)-AMINO]-3-PHENYL-PROPIONIC ACID
C29 H21 Cl2 N O4 S
YBULOUKTPCHXAL-DEOSSOPVSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
154 PDBBind:  1NHV Ki: 2200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.251 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.501α = 90
b = 107.826β = 90
c = 126.535γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description