3P8N

Crystal structure of HCV NS3/NS4A protease complexed with BI 201335


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Combined X-ray, NMR, and kinetic analyses reveal uncommon binding characteristics of the hepatitis C virus NS3-NS4A protease inhibitor BI 201335.

Lemke, C.T.Goudreau, N.Zhao, S.Hucke, O.Thibeault, D.Llinas-Brunet, M.White, P.W.

(2011) J Biol Chem 286: 11434-11443

  • DOI: 10.1074/jbc.M110.211417
  • Primary Citation of Related Structures:  
    3P8N, 3P8O

  • PubMed Abstract: 
  • Hepatitis C virus infection, a major cause of liver disease worldwide, is curable, but currently approved therapies have suboptimal efficacy. Supplementing these therapies with direct-acting antiviral agents has the potential to considerably improve ...

    Hepatitis C virus infection, a major cause of liver disease worldwide, is curable, but currently approved therapies have suboptimal efficacy. Supplementing these therapies with direct-acting antiviral agents has the potential to considerably improve treatment prospects for hepatitis C virus-infected patients. The critical role played by the viral NS3 protease makes it an attractive target, and despite its shallow, solvent-exposed active site, several potent NS3 protease inhibitors are currently in the clinic. BI 201335, which is progressing through Phase IIb trials, contains a unique C-terminal carboxylic acid that binds noncovalently to the active site and a bromo-quinoline substitution on its proline residue that provides significant potency. In this work we have used stopped flow kinetics, x-ray crystallography, and NMR to characterize these distinctive features. Key findings include: slow association and dissociation rates within a single-step binding mechanism; the critical involvement of water molecules in acid binding; and protein side chain rearrangements, a bromine-oxygen halogen bond, and profound pK(a) changes within the catalytic triad associated with binding of the bromo-quinoline moiety.


    Organizational Affiliation

    Boehringer Ingelheim (Canada) Ltd., Research and Development, Laval, Quebec, Canada. christopher.lemke@boehringer-ingelheim.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HCV serine protease NS3AB186Hepatitis C virus (isolate Japanese)Mutation(s): 0 
Gene Names: POLG_HCVJA
EC: 3.4.21.98 (PDB Primary Data), 3.4.22 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese))
Explore P26662 
Go to UniProtKB:  P26662
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HCV non-structural protein 4ACD17N/AMutation(s): 0 
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese))
Explore P26662 
Go to UniProtKB:  P26662
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L4T
Query on L4T

Download CCD File 
A, B
N-[(cyclopentyloxy)carbonyl]-3-methyl-L-valyl-(4R)-4-[(8-bromo-7-methoxy-2-{2-[(2-methylpropanoyl)amino]-1,3-thiazol-4-yl}quinolin-4-yl)oxy]-N-[(1R,2S)-1-carboxy-2-ethenylcyclopropyl]-L-prolinamide
C40 H49 Br N6 O9 S
LLGDPTDZOVKFDU-XUHJSTDZSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L4TKi :  0.5299999713897705   nM  PDBBind
L4TKi:  0.5299999713897705   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.203 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.874α = 90
b = 94.874β = 90
c = 81.88γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2010-10-14 
  • Released Date: 2011-01-26 
  • Deposition Author(s): Lemke, C.T.

Revision History 

  • Version 1.0: 2011-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-12-12
    Changes: Other
  • Version 1.3: 2017-11-08
    Changes: Advisory, Refinement description