6W4G

Hepatitis C virus polymerase NS5B with RO inhibitor for SAR studies


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Identification of Noncompetitive Protein-Ligand Interactions for Structural Optimization.

Tosstorff, A.Cole, J.C.Taylor, R.Harris, S.F.Kuhn, B.

(2020) J Chem Inf Model 60: 6595-6611

  • DOI: 10.1021/acs.jcim.0c00858
  • Primary Citation of Related Structures:  
    6W4G

  • PubMed Abstract: 
  • For efficient structure-guided drug design, it is important to have an excellent understanding of the quality of interactions between the target receptor and bound ligands. Identification and characterization of poor intermolecular contacts offers the possibility to focus design efforts directly on ligand regions with suboptimal molecular recognition ...

    For efficient structure-guided drug design, it is important to have an excellent understanding of the quality of interactions between the target receptor and bound ligands. Identification and characterization of poor intermolecular contacts offers the possibility to focus design efforts directly on ligand regions with suboptimal molecular recognition. To enable a more straightforward identification of these in a structural model, we use a suitably enhanced version of our previously introduced statistical ratio of frequencies ( R F ) approach. This allows us to highlight protein-ligand interactions and geometries that occur much less often in the Protein Data Bank than would be expected from the exposed surface areas of the interacting atoms. We provide a comprehensive overview of such noncompetitive interactions and geometries for a set of common ligand substituents. Through retrospective case studies on congeneric series and single-point mutations for several pharmaceutical targets, we illustrate how knowledge of noncompetitive interactions could be exploited in the drug design process.


    Organizational Affiliation

    Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NS5BA, B568Hepatitis C virus (isolate BK)Mutation(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
SL4 (Subject of Investigation/LOI)
Query on SL4

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]5-[[(2~{S})-4-[1,1-bis(oxidanylidene)-1,2-benzothiazol-3-yl]-2-~{tert}-butyl-3-oxidanyl-5-oxidanylidene-2~{H}-pyrrol-1-yl]methyl]-2-fluoranyl-benzenecarbonitrile
C23 H20 F N3 O4 S
AYAOVCPFNMGVER-OAQYLSRUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.478α = 90
b = 104.704β = 90
c = 126.119γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2020-03-10 
  • Released Date: 2020-11-04 
  • Deposition Author(s): Harris, S.F.

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references