4CDW

Crystal structure of human Enterovirus 71 in complex with the uncoating inhibitor GPP4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.283 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

More-Powerful Virus Inhibitors from Structure-Based Analysis of Hev71 Capsid-Binding Molecules

De Colibus, L.Wang, X.Spyrou, J.A.B.Kelly, J.Ren, J.Grimes, J.Puerstinger, G.Stonehouse, N.Walter, T.S.Hu, Z.Wang, J.Li, X.Peng, W.Rowlands, D.J.Fry, E.E.Rao, Z.Stuart, D.I.

(2014) Nat.Struct.Mol.Biol. 21: 282

  • DOI: 10.1038/nsmb.2769
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Enterovirus 71 (HEV71) epidemics in children and infants result mainly in mild symptoms; however, especially in the Asia-Pacific region, infection can be fatal. At present, no therapies are available. We have used structural analysis of the complete ...

    Enterovirus 71 (HEV71) epidemics in children and infants result mainly in mild symptoms; however, especially in the Asia-Pacific region, infection can be fatal. At present, no therapies are available. We have used structural analysis of the complete virus to guide the design of HEV71 inhibitors. Analysis of complexes with four 3-(4-pyridyl)-2-imidazolidinone derivatives with varying anti-HEV71 activities pinpointed key structure-activity correlates. We then identified additional potentially beneficial substitutions, developed methods to reliably triage compounds by quantum mechanics-enhanced ligand docking and synthesized two candidates. Structural analysis and in vitro assays confirmed the predicted binding modes and their ability to block viral infection. One ligand (with IC50 of 25 pM) is an order of magnitude more potent than the best previously reported inhibitor and is also more soluble. Our approach may be useful in the design of effective drugs for enterovirus infections.


    Related Citations: 
    • A Sensor-Adaptor Mechanism for Enterovirus Uncoating from Structures of Ev71.
      Wang, X.,Peng, W.,Ren, J.,Hu, Z.,Xu, J.,Lou, Z.,Li, X.,Yin, W.,Shen, X.,Porta, C.,Walter, T.S.,Evans, G.,Axford, D.,Owen, R.,Rowlands, D.J.,Wang, J.,Stuart, D.I.,Fry, E.E.,Rao, Z.
      (2012) Nat.Struct.Mol.Biol. 19: 424


    Organizational Affiliation

    Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VP1
A
297Enterovirus A71Mutation(s): 0 
Find proteins for B2ZUN0 (Enterovirus A71)
Go to UniProtKB:  B2ZUN0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VP2
B
254Enterovirus A71Mutation(s): 0 
Find proteins for B2ZUN0 (Enterovirus A71)
Go to UniProtKB:  B2ZUN0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VP3
C
242Enterovirus A71Mutation(s): 0 
Find proteins for B2ZUN0 (Enterovirus A71)
Go to UniProtKB:  B2ZUN0
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
VP4
D
69Enterovirus A71Mutation(s): 0 
Find proteins for B2ZUN0 (Enterovirus A71)
Go to UniProtKB:  B2ZUN0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
VR2
Query on VR2

Download SDF File 
Download CCD File 
A
1-[(3S)-5-(4-iodanylphenoxy)-3-methyl-pentyl]-3-pyridin-4-yl-imidazolidin-2-one
C20 H24 I N3 O2
SVYVYARVADIYRJ-INIZCTEOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.283 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 599.660α = 90.00
b = 599.660β = 90.00
c = 599.660γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
CNSphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-02-19
    Type: Database references
  • Version 1.2: 2014-03-19
    Type: Database references
  • Version 1.3: 2019-01-30
    Type: Data collection, Experimental preparation
  • Version 1.4: 2019-02-06
    Type: Data collection, Experimental preparation