6GZV

Identification of a druggable VP1-VP3 interprotomer pocket in the capsid of enteroviruses


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A novel druggable interprotomer pocket in the capsid of rhino- and enteroviruses.

Abdelnabi, R.Geraets, J.A.Ma, Y.Mirabelli, C.Flatt, J.W.Domanska, A.Delang, L.Jochmans, D.Kumar, T.A.Jayaprakash, V.Sinha, B.N.Leyssen, P.Butcher, S.J.Neyts, J.

(2019) Plos Biol. 17: e3000281-e3000281

  • DOI: 10.1371/journal.pbio.3000281

  • PubMed Abstract: 
  • Rhino- and enteroviruses are important human pathogens, against which no antivirals are available. The best-studied inhibitors are "capsid binders" that fit in a hydrophobic pocket of the viral capsid. Employing a new class of entero-/rhinovirus inhi ...

    Rhino- and enteroviruses are important human pathogens, against which no antivirals are available. The best-studied inhibitors are "capsid binders" that fit in a hydrophobic pocket of the viral capsid. Employing a new class of entero-/rhinovirus inhibitors and by means of cryo-electron microscopy (EM), followed by resistance selection and reverse genetics, we discovered a hitherto unknown druggable pocket that is formed by viral proteins VP1 and VP3 and that is conserved across entero-/rhinovirus species. We propose that these inhibitors stabilize a key region of the virion, thereby preventing the conformational expansion needed for viral RNA release. A medicinal chemistry effort resulted in the identification of analogues targeting this pocket with broad-spectrum activity against Coxsackieviruses B (CVBs) and compounds with activity against enteroviruses (EV) of groups C and D, and even rhinoviruses (RV). Our findings provide novel insights in the biology of the entry of entero-/rhinoviruses and open new avenues for the design of broad-spectrum antivirals against these pathogens.


    Organizational Affiliation

    Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium.,Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland.,Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP1
A
284Coxsackievirus B3 (strain Nancy)Mutation(s): 0 
Find proteins for P03313 (Coxsackievirus B3 (strain Nancy))
Go to UniProtKB:  P03313
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP2
B
263Coxsackievirus B3 (strain Nancy)Mutation(s): 0 
Find proteins for P03313 (Coxsackievirus B3 (strain Nancy))
Go to UniProtKB:  P03313
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP3
C
238Coxsackievirus B3 (strain Nancy)Mutation(s): 0 
Find proteins for P03313 (Coxsackievirus B3 (strain Nancy))
Go to UniProtKB:  P03313
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP4
D
69Coxsackievirus B3 (strain Nancy)Mutation(s): 0 
Find proteins for P03313 (Coxsackievirus B3 (strain Nancy))
Go to UniProtKB:  P03313
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FHK
Query on FHK

Download SDF File 
Download CCD File 
C
4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]benzoic acid
C21 H14 N2 O6 S
KCHARURJHJMOQX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European UnionFinland612308

Revision History 

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-06-12
    Type: Data collection
  • Version 1.2: 2019-06-19
    Type: Data collection, Database references