3SJO

structure of EV71 3C in complex with Rupintrivir (AG7088)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Enterovirus 71 and Coxsackievirus A16 3C Proteases: Binding to Rupintrivir and Their Substrates and Anti-Hand, Foot, and Mouth Disease Virus Drug Design.

Lu, G.Qi, J.Chen, Z.Xu, X.Gao, F.Lin, D.Qian, W.Liu, H.Jiang, H.Yan, J.Gao, G.F.

(2011) J Virol 85: 10319-10331

  • DOI: https://doi.org/10.1128/JVI.00787-11
  • Primary Citation of Related Structures:  
    3SJ8, 3SJ9, 3SJI, 3SJK, 3SJO

  • PubMed Abstract: 

    Enterovirus 71 (EV71) and coxsackievirus A16 (CVA16) are the major causative agents of hand, foot, and mouth disease (HFMD), which is prevalent in Asia. Thus far, there are no prophylactic or therapeutic measures against HFMD. The 3C proteases from EV71 and CVA16 play important roles in viral replication and are therefore ideal drug targets. By using biochemical, mutational, and structural approaches, we broadly characterized both proteases. A series of high-resolution structures of the free or substrate-bound enzymes were solved. These structures, together with our cleavage specificity assay, well explain the marked substrate preferences of both proteases for particular P4, P1, and P1' residue types, as well as the relative malleability of the P2 amino acid. More importantly, the complex structures of EV71 and CVA16 3Cs with rupintrivir, a specific human rhinovirus (HRV) 3C protease inhibitor, were solved. These structures reveal a half-closed S2 subsite and a size-reduced S1' subsite that limit the access of the P1' group of rupintrivir to both enzymes, explaining the reported low inhibition activity of the compound toward EV71 and CVA16. In conclusion, the detailed characterization of both proteases in this study could direct us to a proposal for rational design of EV71/CVA16 3C inhibitors.


  • Organizational Affiliation

    Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C protease
A, B, C, D, E
A, B, C, D, E, F, G, H
190Enterovirus A71Mutation(s): 0 
Gene Names: 3C
EC: 3.4.22.28
UniProt
Find proteins for E0WWC7 (Human enterovirus 71)
Explore E0WWC7 
Go to UniProtKB:  E0WWC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0WWC7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AG7
Query on AG7

Download Ideal Coordinates CCD File 
I [auth A]
J [auth B]
K [auth C]
L [auth D]
M [auth E]
I [auth A],
J [auth B],
K [auth C],
L [auth D],
M [auth E],
N [auth F],
O [auth G],
P [auth H]
4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE-3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO-PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER
C31 H41 F N4 O7
LMIUALQNZXJHOG-IFILWLFVSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
AG7 PDBBind:  3SJO IC50: 1650 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.258α = 89.96
b = 82.171β = 89.99
c = 97.952γ = 90.13
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2011-09-28
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description