Dengue-RdRp3-inhibitor complex co-crystallisation

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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This is version 1.1 of the entry. See complete history


Development and validation of RdRp Screen, a crystallization screen for viral RNA-dependent RNA polymerases.

Riccio, F.Talapatra, S.K.Oxenford, S.Angell, R.Mazzon, M.Kozielski, F.

(2019) Biol Open 8

  • DOI: https://doi.org/10.1242/bio.037663
  • Primary Citation of Related Structures:  
    6H80, 6H9R

  • PubMed Abstract: 

    Members of the Flaviviridae family constitute a severe risk to human health. Whilst effective drugs have been developed against the hepacivirus HCV, no antiviral therapy is currently available for any other viruses, including the flaviviruses dengue (DENV), West Nile and Zika viruses. The RNA-dependent RNA polymerase (RdRp) is responsible for viral replication and represents an excellent therapeutic target with no homologue found in mammals. The identification of compounds targeting the RdRp of other flaviviruses is an active area of research. One of the main factors hampering further developments in the field is the difficulty in obtaining high-quality crystal information that could aid a structure-based drug discovery approach. To address this, we have developed a convenient and economical 96-well screening platform. We validated the screen by successfully obtaining crystals of both native DENV serotype 2 and 3 RdRps under several conditions included in the screen. In addition, we have obtained crystal structures of RdRp3 in complex with a previously identified fragment using both soaking and co-crystallization techniques. This work will streamline and accelerate the generation of crystal structures of viral RdRps and provide the community with a valuable tool to aid the development of structure-based antiviral design.

  • Organizational Affiliation

    Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyprotein635Dengue virus 3 Sri Lanka/1266/2000Mutation(s): 4 
Gene Names: pol
EC: (PDB Primary Data), (PDB Primary Data), (PDB Primary Data), (PDB Primary Data), (PDB Primary Data), (PDB Primary Data)
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
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5V5

Download Ideal Coordinates CCD File 
B [auth A]2-(4-methoxy-3-thiophen-2-yl-phenyl)ethanoic acid
C13 H12 O3 S
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
C4 H10 O3
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.08α = 90
b = 181.25β = 90
c = 57.92γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description