6GZV

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 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: https://doi.org/10.1371/journal.pbio.3000281
  • Primary Citation of Related Structures:  
    6GZV

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP1284Coxsackievirus B3 (strain Nancy)Mutation(s): 0 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P03313 (Coxsackievirus B3 (strain Nancy))
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Go to UniProtKB:  P03313
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UniProt GroupP03313
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP2263Coxsackievirus B3 (strain Nancy)Mutation(s): 0 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P03313 (Coxsackievirus B3 (strain Nancy))
Explore P03313 
Go to UniProtKB:  P03313
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UniProt GroupP03313
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP3238Coxsackievirus B3 (strain Nancy)Mutation(s): 0 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P03313 (Coxsackievirus B3 (strain Nancy))
Explore P03313 
Go to UniProtKB:  P03313
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03313
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP469Coxsackievirus B3 (strain Nancy)Mutation(s): 0 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P03313 (Coxsackievirus B3 (strain Nancy))
Explore P03313 
Go to UniProtKB:  P03313
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03313
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FHK
Query on FHK

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1.beta
MODEL REFINEMENTMDFF0.5
MODEL REFINEMENTCoot0.8.8

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European UnionFinland612308

Revision History  (Full details and data files)

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