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 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acs.jmedchem.6b00143
  • Primary Citation of Related Structures:  
    5HMW, 5HMX, 5HMY, 5HMZ, 5HN0

  • 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 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

    Novartis Institute for Tropical Diseases , 10 Biopolis Road, no. 05-01, Chromos, Singapore 138670, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase NS5635dengue virus type 3Mutation(s): 1 
EC: 2.7.7.48
UniProt
Find proteins for Q6YMS4 (Dengue virus type 3 (strain Sri Lanka/1266/2000))
Explore Q6YMS4 
Go to UniProtKB:  Q6YMS4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6YMS4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LNZ
Query on LNZ

Download Ideal Coordinates CCD File 
D [auth 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
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.875α = 90
b = 175.498β = 90
c = 57.87γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTER-TNTphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2016-05-18
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description