4B73

Discovery of an allosteric mechanism for the regulation of HCV NS3 protein function


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Discovery of an Allosteric Mechanism for the Regulation of Hcv Ns3 Protein Function.

Saalau-Bethell, S.M.Woodhead, A.J.Chessari, G.Carr, M.G.Coyle, J.Graham, B.Hiscock, S.D.Murray, C.W.Pathuri, P.Rich, S.J.Richardson, C.J.Williams, P.A.Jhoti, H.

(2012) Nat Chem Biol 8: 920

  • DOI: https://doi.org/10.1038/nchembio.1081
  • Primary Citation of Related Structures:  
    4B6E, 4B6F, 4B71, 4B73, 4B74, 4B75, 4B76

  • PubMed Abstract: 

    Here we report a highly conserved new binding site located at the interface between the protease and helicase domains of the hepatitis C virus (HCV) NS3 protein. Using a chemical lead, identified by fragment screening and structure-guided design, we demonstrate that this site has a regulatory function on the protease activity via an allosteric mechanism. We propose that compounds binding at this allosteric site inhibit the function of the NS3 protein by stabilizing an inactive conformation and thus represent a new class of direct-acting antiviral agents.


  • Organizational Affiliation

    Astex Pharmaceuticals, Cambridge Science Park, Cambridge, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NON-STRUCTURAL PROTEIN 4A, SERINE PROTEASE NS3
A, B
666Hepatitis C virus (isolate BK)Mutation(s): 0 
EC: 3.4.21.98 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK))
Explore P26663 
Go to UniProtKB:  P26663
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26663
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4VA
Query on 4VA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2S)-4-amino-N-[(1R)-1-(4-chloro-2-fluoro-3-phenoxyphenyl)propyl]-4-oxobutan-2-aminium
C19 H23 Cl F N2 O2
DXPCUPMRYIXTFI-BLLLJJGKSA-O
Binding Affinity Annotations 
IDSourceBinding Affinity
4VA PDBBind:  4B73 Kd: 62 (nM) from 1 assay(s)
Binding MOAD:  4B73 Kd: 62 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.842α = 90
b = 109.496β = 90
c = 141.024γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
CSEARCHphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2012-10-17
    Changes: Database references
  • Version 1.2: 2012-10-31
    Changes: Database references
  • Version 1.3: 2013-02-06
    Changes: Atomic model
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description