4IH7

Hepatitis C Virus polymerase NS5B (BK) with fragment-based compounds


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

De novo fragment design: a medicinal chemistry approach to fragment-based lead generation.

Talamas, F.X.Ao-Ieong, G.Brameld, K.A.Chin, E.de Vicente, J.Dunn, J.P.Ghate, M.Giannetti, A.M.Harris, S.F.Labadie, S.S.Leveque, V.Li, J.Lui, A.S.McCaleb, K.L.Najera, I.Schoenfeld, R.C.Wang, B.Wong, A.

(2013) J.Med.Chem. 56: 3115-3119

  • DOI: 10.1021/jm4002605
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The use of fragments with low binding affinity for their targets as starting points has received much attention recently. Screening of fragment libraries has been the most common method to find attractive starting points. Herein, we describe a unique ...

    The use of fragments with low binding affinity for their targets as starting points has received much attention recently. Screening of fragment libraries has been the most common method to find attractive starting points. Herein, we describe a unique, alternative approach to generating fragment leads. A binding model was developed and a set of guidelines were then selected to use this model to design fragments, enabling our discovery of a novel fragment with high LE.


    Organizational Affiliation

    Hoffmann-La Roche Inc, Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States. franciscotalamas@gmail.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase
A, B
570Hepatitis 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
1ER
Query on 1ER

Download SDF File 
Download CCD File 
A, B
3-(3-tert-butylphenyl)pyridin-2(1H)-one
C15 H17 N O
OCDNGTPNEHVSMA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1ERKd: 5800 nM BINDINGMOAD
1ERKd: 5800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.254α = 90.00
b = 104.919β = 90.00
c = 125.875γ = 90.00
Software Package:
Software NamePurpose
BUSTERphasing
BUSTERrefinement
HKL-2000data reduction
Blu-Icedata collection
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-12-18 
  • Released Date: 2013-07-03 
  • Deposition Author(s): Harris, S.F., Wong, A.

Revision History 

  • Version 1.0: 2013-07-03
    Type: Initial release