6H80

Dengue-RdRp3-inhibitor complex co-crystallisation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 10.1242/bio.037663
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Members of the <i>Flaviviridae </i> family constitute a severe risk to human health. Whilst effective drugs have been developed against the <i>hepacivirus </i> HCV, no antiviral therapy is currently available for any other viruses, including the < ...

    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.,Translational Research Office, UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom.,UCL MRC Laboratory for Molecular Cell Biology, Gower Street, London, WC1E 6BT, United Kingdom.,Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom f.kozielski@ucl.ac.uk s.talapatra@ucl.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Genome polyprotein
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5V5
Query on 5V5

Download SDF File 
Download CCD File 
A
2-(4-methoxy-3-thiophen-2-yl-phenyl)ethanoic acid
C13 H12 O3 S
HCAVDRSGOUZCSD-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.191 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 165.080α = 90.00
b = 181.250β = 90.00
c = 57.920γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release