5EIW

DENGUE 3 NS5 METHYLTRANSFERASE BOUND TO S-ADENOSYL METHIONINE AND FRAGMENT NB3C2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of novel dengue virus NS5 methyltransferase non-nucleoside inhibitors by fragment-based drug design.

Benmansour, F.Trist, I.Coutard, B.Decroly, E.Querat, G.Brancale, A.Barral, K.

(2016) Eur J Med Chem 125: 865-880

  • DOI: 10.1016/j.ejmech.2016.10.007
  • Primary Citation of Related Structures:  
    5E9Q, 5EC8, 5EHI, 5EHG, 5EIW, 5EIF, 5EKX

  • PubMed Abstract: 
  • With the aim to help drug discovery against dengue virus (DENV), a fragment-based drug design approach was applied to identify ligands targeting a main component of DENV replication complex: the NS5 AdoMet-dependent mRNA methyltransferase (MTase) domain, playing an essential role in the RNA capping process ...

    With the aim to help drug discovery against dengue virus (DENV), a fragment-based drug design approach was applied to identify ligands targeting a main component of DENV replication complex: the NS5 AdoMet-dependent mRNA methyltransferase (MTase) domain, playing an essential role in the RNA capping process. Herein, we describe the identification of new inhibitors developed using fragment-based, structure-guided linking and optimization techniques. Thermal-shift assay followed by a fragment-based X-ray crystallographic screening lead to the identification of three fragment hits binding DENV MTase. We considered linking two of them, which bind to proximal sites of the AdoMet binding pocket, in order to improve their potency. X-ray crystallographic structures and computational docking were used to guide the fragment linking, ultimately leading to novel series of non-nucleoside inhibitors of flavivirus MTase, respectively N-phenyl-[(phenylcarbamoyl)amino]benzene-1-sulfonamide and phenyl [(phenylcarbamoyl)amino]benzene-1-sulfonate derivatives, that show a 10-100-fold stronger inhibition of 2'-O-MTase activity compared to the initial fragments.


    Organizational Affiliation

    Aix-Marseille Université, AFMB UMR 7257, 163 Avenue de Luminy, 13288 Marseille cedex 09, France; CNRS, AFMB UMR 7257, 163 Avenue de Luminy, 13288 Marseille cedex 09, France; Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France. Electronic address: karine.barral@inserm.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NS5 methyltransferaseA, B [auth C]276Dengue virus 3Mutation(s): 0 
EC: 2.7.7.48 (PDB Primary Data), 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt)
UniProt
Find proteins for Q6YMS4 (Dengue virus type 3 (strain Sri Lanka/1266/2000))
Explore Q6YMS4 
Go to UniProtKB:  Q6YMS4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
C [auth A], E [auth C]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
X0V
Query on X0V

Download Ideal Coordinates CCD File 
D [auth A]4-(TRIFLUOROMETHYL)BENZENE-1,2-DIAMINE
C7 H7 F3 N2
RQWJHUJJBYMJMN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.26α = 90
b = 184.37β = 90
c = 51.98γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
AutoPROCdata collection
SCALAdata scaling
BUSTERrefinement
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-13-JS07-0006-01

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Advisory, Author supporting evidence, Data collection, Refinement description