3GNV

HCV NS5B polymerase in complex with 1,5 benzodiazepine inhibitor 1b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based design of a benzodiazepine scaffold yields a potent allosteric inhibitor of hepatitis C NS5B RNA polymerase.

Vandyck, K.Cummings, M.D.Nyanguile, O.Boutton, C.W.Vendeville, S.McGowan, D.Devogelaere, B.Amssoms, K.Last, S.Rombauts, K.Tahri, A.Lory, P.Hu, L.Beauchamp, D.A.Simmen, K.Raboisson, P.

(2009) J.Med.Chem. 52: 4099-4102

  • DOI: 10.1021/jm9005548
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • HCV NS5B polymerase, an essential and virus-specific enzyme, is an important target for drug discovery. Using structure-based design, we optimized a 1,5-benzodiazepine NS5B polymerase inhibitor chemotype into a new sulfone-containing scaffold. The de ...

    HCV NS5B polymerase, an essential and virus-specific enzyme, is an important target for drug discovery. Using structure-based design, we optimized a 1,5-benzodiazepine NS5B polymerase inhibitor chemotype into a new sulfone-containing scaffold. The design yielded potent inhibitor (S)-4c (K(D) = 0.79 nM), which has approximately 20-fold greater affinity for NS5B than its carbonyl analogue (R)-2c.


    Organizational Affiliation

    Tibotec BVBA, Generaal de Wittelaan L 11B 3, B-2800 Mechelen, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase
A, B
581Hepatitis 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
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
XNZ
Query on XNZ

Download SDF File 
Download CCD File 
A, B
(11R)-10-acetyl-11-[4-(benzyloxy)-2-chlorophenyl]-6-hydroxy-3,3-dimethyl-2,3,4,5,10,11-hexahydro-1H-dibenzo[b,e][1,4]diazepin-1-one
C30 H29 Cl N2 O4
VZBRCRRODKYBEF-LJAQVGFWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XNZIC50: 93 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 106.291α = 90.00
b = 107.965β = 90.00
c = 133.799γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance