5HMZ

Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 23


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Potent Non-Nucleoside Inhibitors of Dengue Viral RNA-Dependent RNA Polymerase from a Fragment Hit Using Structure-Based Drug Design

Yokokawa, F.Nilar, S.Noble, C.G.Lim, S.P.Rao, R.Tania, S.Wang, G.Lee, G.Hunziker, J.Karuna, R.Manjunatha, U.Shi, P.Y.Smith, P.W.

(2016) J.Med.Chem. 59: 3935-3952

  • DOI: 10.1021/acs.jmedchem.6b00143
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The discovery and optimization of non-nucleoside dengue viral RNA-dependent-RNA polymerase (RdRp) inhibitors are described. An X-ray-based fragment screen of Novartis' fragment collection resulted in the identification of a biphenyl acetic acid fragm ...

    The discovery and optimization of non-nucleoside dengue viral RNA-dependent-RNA polymerase (RdRp) inhibitors are described. An X-ray-based fragment screen of Novartis' fragment collection resulted in the identification of a biphenyl acetic acid fragment 3, which bound in the palm subdomain of RdRp. Subsequent optimization of the fragment hit 3, relying on structure-based design, resulted in a >1000-fold improvement in potency in vitro and acquired antidengue activity against all four serotypes with low micromolar EC50 in cell-based assays. The lead candidate 27 interacts with a novel binding pocket in the palm subdomain of the RdRp and exerts a promising activity against all clinically relevant dengue serotypes.


    Organizational Affiliation

    Department of Biochemistry & Molecular Biology, Department of Phamarcology & Toxicology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch , Galveston, Texas 77555, United States.,Novartis Institute for Tropical Diseases , 10 Biopolis Road, no. 05-01, Chromos, Singapore 138670, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase NS5
A
635Dengue virus type 3 (strain Sri Lanka/1266/2000)Mutation(s): 0 
Gene Names: pol
Find proteins for Q6YMS4 (Dengue virus type 3 (strain Sri Lanka/1266/2000))
Go to UniProtKB:  Q6YMS4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
LNZ
Query on LNZ

Download SDF File 
Download CCD File 
A
5-(5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl)-4-methoxy-2-methyl-N-(methylsulfonyl)benzamide
C17 H17 N O5 S2
BQEHLOAHCIMXML-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.181 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 160.875α = 90.00
b = 175.498β = 90.00
c = 57.870γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
BUSTERrefinement
BUSTER-TNTphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-01-17 
  • Released Date: 2016-03-30 
  • Deposition Author(s): Noble, C.G.

Revision History 

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2016-05-18
    Type: Database references