5K5M

Co-Crystal Structure of Dengue Virus Serotype 2 RNA Dependent RNA Polymerase with Compound 27


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling.

Lim, S.P.Noble, C.G.Seh, C.C.Soh, T.S.El Sahili, A.Chan, G.K.Lescar, J.Arora, R.Benson, T.Nilar, S.Manjunatha, U.Wan, K.F.Dong, H.Xie, X.Shi, P.Y.Yokokawa, F.

(2016) Plos Pathog. 12: e1005737-e1005737

  • DOI: 10.1371/journal.ppat.1005737
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Flaviviruses comprise major emerging pathogens such as dengue virus (DENV) or Zika virus (ZIKV). The flavivirus RNA genome is replicated by the RNA-dependent-RNA polymerase (RdRp) domain of non-structural protein 5 (NS5). This essential enzymatic act ...

    Flaviviruses comprise major emerging pathogens such as dengue virus (DENV) or Zika virus (ZIKV). The flavivirus RNA genome is replicated by the RNA-dependent-RNA polymerase (RdRp) domain of non-structural protein 5 (NS5). This essential enzymatic activity renders the RdRp attractive for antiviral therapy. NS5 synthesizes viral RNA via a "de novo" initiation mechanism. Crystal structures of the flavivirus RdRp revealed a "closed" conformation reminiscent of a pre-initiation state, with a well ordered priming loop that extrudes from the thumb subdomain into the dsRNA exit tunnel, close to the "GDD" active site. To-date, no allosteric pockets have been identified for the RdRp, and compound screening campaigns did not yield suitable drug candidates. Using fragment-based screening via X-ray crystallography, we found a fragment that bound to a pocket of the apo-DENV RdRp close to its active site (termed "N pocket"). Structure-guided improvements yielded DENV pan-serotype inhibitors of the RdRp de novo initiation activity with nano-molar potency that also impeded elongation activity at micro-molar concentrations. Inhibitors exhibited mixed inhibition kinetics with respect to competition with the RNA or GTP substrate. The best compounds have EC50 values of 1-2 μM against all four DENV serotypes in cell culture assays. Genome-sequencing of compound-resistant DENV replicons, identified amino acid changes that mapped to the N pocket. Since inhibitors bind at the thumb/palm interface of the RdRp, this class of compounds is proposed to hinder RdRp conformational changes during its transition from initiation to elongation. This is the first report of a class of pan-serotype and cell-active DENV RdRp inhibitors. Given the evolutionary conservation of residues lining the N pocket, these molecules offer insights to treat other serious conditions caused by flaviviruses.


    Organizational Affiliation

    Novartis Institute for Tropical Diseases, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA Dependent RNA Polymerase
A
635Dengue virus 2Mutation(s): 0 
Find proteins for A0A097PIE2 (Dengue virus 2)
Go to UniProtKB:  A0A097PIE2
Small Molecules
Ligands 3 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
68T
Query on 68T

Download SDF File 
Download CCD File 
A
5-[5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl]-2,4-dimethoxy-N-[(3-methoxyphenyl)sulfonyl]benzamide
C23 H21 N O7 S2
GFHHFWCGCHIDBF-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 82.140α = 90.00
b = 115.770β = 90.00
c = 148.590γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-24
    Type: Initial release