5FPY

Structure of hepatitis C virus (HCV) full-length NS3 complex with small-molecule ligand 5-bromo-1-methyl-1H-indole-2-carboxylic acid (AT21457) in an alternate binding site.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Detection of Secondary Binding Sites in Proteins Using Fragment Screening.

Ludlow, R.F.Verdonk, M.L.Saini, H.K.Tickle, I.J.Jhoti, H.

(2015) Proc.Natl.Acad.Sci.USA 112: 15910

  • DOI: 10.1073/pnas.1518946112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins ...

    Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins at specific locations on a protein that can modulate function. Often, these additional secondary binding sites appear separate to the primary binding site, which, for example for an enzyme, may bind a substrate. In previous work, we have uncovered several examples in which secondary binding sites were discovered on proteins using fragment screening approaches. In each case, we were able to establish that the newly identified secondary binding site was biologically relevant as it was able to modulate function by the binding of a small molecule. In this study, we investigate how often secondary binding sites are located on proteins by analyzing 24 protein targets for which we have performed a fragment screen using X-ray crystallography. Our analysis shows that, surprisingly, the majority of proteins contain secondary binding sites based on their ability to bind fragments. Furthermore, sequence analysis of these previously unknown sites indicate high conservation, which suggests that they may have a biological function, perhaps via an allosteric mechanism. Comparing the physicochemical properties of the secondary sites with known primary ligand binding sites also shows broad similarities indicating that many of the secondary sites may be druggable in nature with small molecules that could provide new opportunities to modulate potential therapeutic targets.


    Related Citations: 
    • 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
    • Molecular Views of Viral Polyprotein Processing Revealed by the Crystal Structure of the Hepatitis C Virus Bifunctional Protease-Helicase.
      Yao, N.,Reichert, P.,Taremi, S.S.,Prosise, W.W.,Weber, P.C.
      (1999) Structure 7: 1353


    Organizational Affiliation

    Astex Pharmaceuticals, Cambridge CB4 0QA, United Kingdom.,Astex Pharmaceuticals, Cambridge CB4 0QA, United Kingdom harren.jhoti@astx.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE PROTEASE NS3
A, B
666Hepatitis C virus genotype 1b (isolate BK)Mutation(s): 0 
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK))
Go to UniProtKB:  P26663
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R2N
Query on R2N

Download SDF File 
Download CCD File 
A, B
5-bromo-1-methyl-1H-indole-2-carboxylic acid
C10 H8 Br N O2
GCGFIFNQFLLJIR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 90.902α = 90.00
b = 109.773β = 90.00
c = 142.004γ = 90.00
Software Package:
Software NamePurpose
CSEARCHphasing
MOSFLMdata reduction
BUSTERrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2016-01-13
    Type: Database references