3MWW

Crystal structure of HCV NS5B polymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Importance of ligand bioactive conformation in the discovery of potent indole-diamide inhibitors of the hepatitis C virus NS5B.

LaPlante, S.R.Gillard, J.R.Jakalian, A.Aubry, N.Coulombe, R.Brochu, C.Tsantrizos, Y.S.Poirier, M.Kukolj, G.Beaulieu, P.L.

(2010) J.Am.Chem.Soc. 132: 15204-15212

  • DOI: 10.1021/ja101358s
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Significant advances have led to receptor induced-fit and conformational selection models for describing bimolecular recognition, but a more comprehensive view must evolve to also include ligand shape and conformational changes. Here, we describe an ...

    Significant advances have led to receptor induced-fit and conformational selection models for describing bimolecular recognition, but a more comprehensive view must evolve to also include ligand shape and conformational changes. Here, we describe an example where a ligand's "structural hinge" influences potency by inducing an "L-shape" bioactive conformation, and due to its solvent exposure in the complex, reasonable conformation-activity-relationships can be qualitatively attributed. From a ligand design perspective, this feature was exploited by successful linker hopping to an alternate "structural hinge" that led to a new and promising chemical series which matched the ligand bioactive conformation and the pocket bioactive space. Using a combination of X-ray crystallography, NMR and modeling with support from binding-site resistance mutant studies and photoaffinity labeling experiments, we were able to derive inhibitor-polymerase complexes for various chemical series.


    Organizational Affiliation

    Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard St., Laval, Quebec, Canada, H7S2G5. steven.laplante@boehringer-ingelheim.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Genome polyprotein
A, B
576Hepatitis C virus genotype 1b (strain HC-J4)Mutation(s): 0 
Find proteins for O92972 (Hepatitis C virus genotype 1b (strain HC-J4))
Go to UniProtKB:  O92972
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BIW
Query on BIW

Download SDF File 
Download CCD File 
B
1-[2-(4-carboxypiperidin-1-yl)-2-oxoethyl]-3-cyclohexyl-2-furan-3-yl-1H-indole-6-carboxylic acid
C27 H30 N2 O6
AVHJWNFYNLONQR-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BIWIC50: 57 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 105.120α = 90.00
b = 106.550β = 90.00
c = 133.460γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
HKL-2000data reduction
CrystalCleardata collection
CNSphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-05-06 
  • Released Date: 2010-10-27 
  • Deposition Author(s): Coulombe, R.

Revision History 

  • Version 1.0: 2010-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description