4WM8

Crystal Structure of Human Enterovirus D68


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.275 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1126/science.1261962
  • Primary Citation of Related Structures:  

  • 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-bin ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VP1
A
297Enterovirus D68Mutation(s): 0 
Gene Names: VP1
Find proteins for Q9YLJ3 (Enterovirus D68)
Go to UniProtKB:  Q9YLJ3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VP2
B
248Enterovirus D68Mutation(s): 0 
Find proteins for Q68T42 (Enterovirus D68)
Go to UniProtKB:  Q68T42
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VP3
C
247Enterovirus D68Mutation(s): 0 
Find proteins for Q68T42 (Enterovirus D68)
Go to UniProtKB:  Q68T42
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
VP4
D
68Enterovirus D68Mutation(s): 0 
Find proteins for Q8QWD4 (Enterovirus D68)
Go to UniProtKB:  Q8QWD4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DKA
Query on DKA

Download SDF File 
Download CCD File 
A
DECANOIC ACID
C10 H20 O2
GHVNFZFCNZKVNT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.275 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 327.000α = 90.00
b = 347.800β = 90.00
c = 357.100γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
HKL-2000data reduction
HKL-3000phasing
PDB_EXTRACTdata extraction
CNSrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI11219

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Other, Refinement description, Source and taxonomy