4IH6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    4IH5, 4IH6, 4IH7

  • 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, alternative approach to generating fragment leads ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymeraseA, B570Hepatitis C virus (isolate BK)Mutation(s): 0 
Gene Names: NS5B
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1EP (Subject of Investigation/LOI)
Query on 1EP

Download Ideal Coordinates CCD File 
C [auth A], D [auth B](5S)-3-(4-tert-butylbenzyl)-5-(propan-2-yl)imidazolidine-2,4-dione
C17 H24 N2 O2
CTDZHQXPMZUNNH-AWEZNQCLSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1EP Binding MOAD:  4IH6 Kd: 1.80e+4 (nM) from 1 assay(s)
PDBBind:  4IH6 Kd: 1.80e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.66α = 90
b = 85.61β = 93.25
c = 115.23γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
BUSTERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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