4CDU

Crystal structure of human Enterovirus 71 in complex with the uncoating inhibitor GPP3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.278 

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

    National Institutes for Food and Drug Control, No. 2, TiantanXili, Beijing, China.,Department of Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, Austria.,Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing, China.,National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China.,Diamond Light Sources, Harwell Science and Innovation Campus, Didcot, UK.,School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.,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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YM2
Query on YM2

Download SDF File 
Download CCD File 
A
1-[(3S)-5-[4-[(E)-ETHOXYIMINOMETHYL]PHENOXY]-3-METHYL-PENTYL]-3-PYRIDIN-4-YL-IMIDAZOLIDIN-2-ONE
C23 H30 N4 O3
IRYPPICIQPYQGY-YSRPOPIVSA-N
 Ligand Interaction
NA
Query on NA

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

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.278 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 599.681α = 90.00
b = 599.681β = 90.00
c = 599.681γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSphasing
CNSrefinement
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