7H3M

Group deposition for crystallographic fragment screening of Coxsackievirus A16 (G-10) 2A protease -- Crystal structure of Coxsackievirus A16 (G-10) 2A protease in complex with Z760031264 (A71EV2A-x0432)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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Ligand Structure Quality Assessment 


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Literature

Crystallographic Fragment Screen of Coxsackievirus A16 2A Protease identifies new opportunities for the development of broad-spectrum anti-enterovirals.

Lithgo, R.M.Tomlinson, C.W.E.Fairhead, M.Winokan, M.Thompson, W.Wild, C.Aschenbrenner, J.C.Balcomb, B.H.Marples, P.G.Chandran, A.V.Golding, M.Koekemoer, L.Williams, E.P.Wang, S.Ni, X.MacLean, E.Giroud, C.Godoy, A.S.Xavier, M.A.Walsh, M.Fearon, D.von Delft, F.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.04.29.591684
  • Primary Citation of Related Structures:  
    7GNV, 7GNW, 7GNX, 7GNY, 7GNZ, 7GO0, 7GO1, 7GO2, 7GO3, 7GO4, 7GO5, 7GO6, 7GO7, 7GO8, 7GO9, 7GOA, 7GOB, 7GOC, 7GOD, 7GOE, 7GOF, 7GOG, 7GOH, 7GOI, 7GOJ, 7GOK, 7GOL, 7GOM, 7GON, 7GOO, 7GOP, 7GOQ, 7GOR, 7GOS, 7GOT, 7GOU, 7GOV, 7GOW, 7GOX, 7GOY, 7GOZ, 7GP0, 7GP1, 7GP2, 7GP3, 7GP4, 7GP5, 7GP6, 7GP7, 7GP8

  • PubMed Abstract: 

    Enteroviruses are the causative agents of paediatric hand-foot-and-mouth disease, and a target for pandemic preparedness due to the risk of higher order complications in a large-scale outbreak. The 2A protease of these viruses is responsible for the self-cleavage of the poly protein, allowing for correct folding and assembly of capsid proteins in the final stages of viral replication. These 2A proteases are highly conserved between Enterovirus species, such as Enterovirus A71 and Coxsackievirus A16 . Inhibition of the 2A protease deranges capsid folding and assembly, preventing formation of mature virions in host cells and making the protease a valuable target for antiviral activity. Herein, we describe a crystallographic fragment screening campaign that identified 75 fragments which bind to the 2A protease including 38 unique compounds shown to bind within the active site. These fragments reveal a path for the development of non-peptidomimetic inhibitors of the 2A protease with broad-spectrum anti-enteroviral activity.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protease 2A150Coxsackievirus A16Mutation(s): 0 
EC: 3.4.22.29
UniProt
Find proteins for Q65900 (Coxsackievirus A16 (strain G-10))
Explore Q65900 
Go to UniProtKB:  Q65900
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ65900
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TJL
Query on TJL

Download Ideal Coordinates CCD File 
B [auth A]4-(1,2,4-oxadiazol-5-yl)aniline
C8 H7 N3 O
LKIGQRFSSGGKQW-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.691α = 90
b = 60.79β = 93.03
c = 32.339γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

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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 StatesU19AI171399

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Database references, Structure summary