3U4R

Novel HCV NS5B polymerase Inhibitors: Discovery of Indole C2 Acyl sulfonamides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

II. Novel HCV NS5B polymerase inhibitors: Discovery of indole C2 acyl sulfonamides.

Anilkumar, G.N.Selyutin, O.Rosenblum, S.B.Zeng, Q.Jiang, Y.Chan, T.Y.Pu, H.Wang, L.Bennett, F.Chen, K.X.Lesburg, C.A.Duca, J.Gavalas, S.Huang, Y.Pinto, P.Sannigrahi, M.Velazquez, F.Venkatraman, S.Vibulbhan, B.Agrawal, S.Ferrari, E.Jiang, C.K.Huang, H.C.Shih, N.Y.George Njoroge, F.Kozlowski, J.A.

(2012) Bioorg Med Chem Lett 22: 713-717

  • DOI: 10.1016/j.bmcl.2011.10.041
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Development of SAR at the C2 position of indole lead 1, a palm site inhibitor of HCV NS5B polymerase (NS5B IC(50)=0.053μM, replicon EC(50)=4.8μM), is described. Initial screening identified an acyl sulfonamide moiety as an isostere for the C2 carboxy ...

    Development of SAR at the C2 position of indole lead 1, a palm site inhibitor of HCV NS5B polymerase (NS5B IC(50)=0.053μM, replicon EC(50)=4.8μM), is described. Initial screening identified an acyl sulfonamide moiety as an isostere for the C2 carboxylic acid group. Further SAR investigation resulted in identification of acyl sufonamide analog 7q (NS5B IC(50)=0.039μM, replicon EC(50)=0.011μM) with >100-fold improved replicon activity.


    Organizational Affiliation

    Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. gopinadhan.anilkumar@Merck.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase
A, B
578Hepatitis C virus isolate HC-J4Mutation(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 O92972 (Hepatitis C virus genotype 1b (strain HC-J4))
Go to UniProtKB:  O92972
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
08F
Query on 08F

Download CCD File 
A, B
1-[(2-aminopyridin-4-yl)methyl]-5-chloro-N-({3-[(methylsulfonyl)amino]phenyl}sulfonyl)-3-(2-oxo-1,2-dihydropyridin-3-yl)-1H-indole-2-carboxamide
C27 H23 Cl N6 O6 S2
CDTLONANIBXQJQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
08FIC50:  39   nM  Binding MOAD
08FIC50:  39   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.922α = 90
b = 106.681β = 90
c = 134.317γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
autoBUSTERmodel building
BUSTERrefinement
CrystalCleardata reduction
CrystalCleardata scaling
autoBUSTERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2012-01-11
    Changes: Database references