4IH7

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

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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)  |  3D 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26663
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1ER
Query on 1ER
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		3-(3-tert-butylphenyl)pyridin-2(1H)-one
C15 H17 N O
OCDNGTPNEHVSMA-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1ER Binding MOAD:  4IH7 Kd: 5800 (nM) from 1 assay(s)
PDBBind:  4IH7 Kd: 5800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.254α = 90
b = 104.919β = 90
c = 125.875γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
BUSTERphasing
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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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