3CIZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 

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Ligand Structure Quality Assessment 


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:  
    3CIZ, 3CJ0, 3CJ2, 3CJ3, 3CJ4, 3CJ5

  • 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 polymeraseA, B576Hepatitis 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)
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SX1 (Subject of Investigation/LOI)
Query on SX1

Download Ideal Coordinates CCD File 
E [auth B]2-amino-5-bromobenzoic acid
C7 H6 Br N O2
CUKXRHLWPSBCTI-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.055α = 90
b = 106.454β = 90
c = 127.051γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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