3CJ4

Crystal structure of hepatitis c virus rna-dependent rna polymerase ns5b in complex with optimized small molecule fragments


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Fragment-based discovery of hepatitis C virus NS5b RNA polymerase inhibitors.

Antonysamy, S.S.Aubol, B.Blaney, J.Browner, M.F.Giannetti, A.M.Harris, S.F.Hebert, N.Hendle, J.Hopkins, S.Jefferson, E.Kissinger, C.Leveque, V.Marciano, D.McGee, E.Najera, I.Nolan, B.Tomimoto, M.Torres, E.Wright, T.

(2008) Bioorg Med Chem Lett 18: 2990-2995

  • DOI: 10.1016/j.bmcl.2008.03.056
  • Primary Citation of Related Structures:  
    3CJ2, 3CJ3, 3CJ4, 3CJ5, 3CJ0, 3CIZ

  • PubMed Abstract: 
  • Non-nucleoside inhibitors of HCV NS5b RNA polymerase were discovered by a fragment-based lead discovery approach, beginning with crystallographic fragment screening. The NS5b binding affinity and biochemical activity of fragment hits and inhibitors was determined by surface plasmon resonance (Biacore) and an enzyme inhibition assay, respectively ...

    Non-nucleoside inhibitors of HCV NS5b RNA polymerase were discovered by a fragment-based lead discovery approach, beginning with crystallographic fragment screening. The NS5b binding affinity and biochemical activity of fragment hits and inhibitors was determined by surface plasmon resonance (Biacore) and an enzyme inhibition assay, respectively. Crystallographic fragment screening hits with approximately 1-10mM binding affinity (K(D)) were iteratively optimized to give leads with approximately 200nM biochemical activity and low microM cellular activity in a Replicon assay.


    Organizational Affiliation

    Medicinal Chemistry, SGX Pharmaceuticals, Inc., 10505 Roselle Street, San Diego, CA 92121, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymerase AB576Hepatitis C virus subtype 1bMutation(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)
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SX5
Query on SX5

Download Ideal Coordinates CCD File 
A, B
4-[(4-bromo-2-{[(3R,5S)-3,5-dimethylpiperidin-1-yl]carbonyl}phenyl)amino]-4-oxobutanoic acid
C18 H23 Br N2 O4
JSVSGWHGYIDZFX-TXEJJXNPSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SX5Kd :  310   nM  PDBBind
SX5IC50:  1000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.143α = 90
b = 86.259β = 93.31
c = 116.141γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2008-03-12 
  • Released Date: 2008-04-15 
  • Deposition Author(s): Antonysamy, s.s.

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance