4WM7

Crystal Structure of Human Enterovirus D68 in Complex with Pleconaril


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.235 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Virus structure. Structure and inhibition of EV-D68, a virus that causes respiratory illness in children.

Liu, Y.Sheng, J.Fokine, A.Meng, G.Shin, W.H.Long, F.Kuhn, R.J.Kihara, D.Rossmann, M.G.

(2015) Science 347: 71-74

  • DOI: https://doi.org/10.1126/science.1261962
  • Primary Citation of Related Structures:  
    4WM7, 4WM8

  • PubMed Abstract: 

    Enterovirus D68 (EV-D68) is a member of Picornaviridae and is a causative agent of recent outbreaks of respiratory illness in children in the United States. We report here the crystal structures of EV-D68 and its complex with pleconaril, a capsid-binding compound that had been developed as an anti-rhinovirus drug. The hydrophobic drug-binding pocket in viral protein 1 contained density that is consistent with a fatty acid of about 10 carbon atoms. This density could be displaced by pleconaril. We also showed that pleconaril inhibits EV-D68 at a half-maximal effective concentration of 430 nanomolar and might, therefore, be a possible drug candidate to alleviate EV-D68 outbreaks.


  • Organizational Affiliation

    Department of Biological Sciences, Hockmeyer Hall of Structural Biology, 240 South Martin Jischke Drive, Purdue University, West Lafayette, IN 47907, USA. Department of Computer Science, 305 North University Street, Purdue University, West Lafayette, IN 47907, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VP1297enterovirus D68Mutation(s): 0 
UniProt
Find proteins for Q9YLJ3 (Human enterovirus D68)
Explore Q9YLJ3 
Go to UniProtKB:  Q9YLJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YLJ3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VP2248enterovirus D68Mutation(s): 0 
UniProt
Find proteins for Q68T42 (Human enterovirus D68)
Explore Q68T42 
Go to UniProtKB:  Q68T42
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ68T42
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VP3247enterovirus D68Mutation(s): 0 
UniProt
Find proteins for Q68T42 (Human enterovirus D68)
Explore Q68T42 
Go to UniProtKB:  Q68T42
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ68T42
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
VP468enterovirus D68Mutation(s): 0 
UniProt
Find proteins for Q8QWD4 (Human enterovirus D68)
Explore Q8QWD4 
Go to UniProtKB:  Q8QWD4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8QWD4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
W11
Query on W11

Download Ideal Coordinates CCD File 
E [auth A]3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE
C18 H18 F3 N3 O3
KQOXLKOJHVFTRN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.235 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 323.2α = 90
b = 346.1β = 90
c = 355.5γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI11219

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Refinement description