3U4O

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.168 

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
  • Primary Citation of Related Structures:  

  • 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 genotype 1b (strain HC-J4)Mutation(s): 0 
Find proteins for O92972 (Hepatitis C virus genotype 1b (strain HC-J4))
Go to UniProtKB:  O92972
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
08E
Query on 08E

Download SDF File 
Download CCD File 
A, B
1-[(2-aminopyridin-4-yl)methyl]-5-chloro-3-(2-oxo-1,2-dihydropyridin-3-yl)-1H-indole-2-carboxylic acid
C20 H15 Cl N4 O3
XPHRQEMVNFKEIN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
08EIC50: 53 nM BINDINGMOAD
08EIC50: 53 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 90.760α = 90.00
b = 106.790β = 90.00
c = 133.820γ = 90.00
Software Package:
Software NamePurpose
AutoPROCdata scaling
autoBUSTERphasing
JDirectordata collection
BUSTERrefinement
autoBUSTERmodel building
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

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