7DNC

Crystal structure of EV71 3C proteinase in complex with a novel inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Design, Synthesis, and Biological Evaluation of Peptidomimetic Aldehydes as Broad-Spectrum Inhibitors against Enterovirus and SARS-CoV-2.

Dai, W.Jochmans, D.Xie, H.Yang, H.Li, J.Su, H.Chang, D.Wang, J.Peng, J.Zhu, L.Nian, Y.Hilgenfeld, R.Jiang, H.Chen, K.Zhang, L.Xu, Y.Neyts, J.Liu, H.

(2022) J Med Chem 65: 2794-2808

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c02258
  • Primary Citation of Related Structures:  
    7DNC

  • PubMed Abstract: 

    A novel series of peptidomimetic aldehydes was designed and synthesized to target 3C protease (3C pro ) of enterovirus 71 (EV71). Most of the compounds exhibited high antiviral activity, and among them, compound 18p demonstrated potent enzyme inhibitory activity and broad-spectrum antiviral activity on a panel of enteroviruses and rhinoviruses. The crystal structure of EV71 3C pro in complex with 18p determined at a resolution of 1.2 Å revealed that 18p covalently linked to the catalytic Cys147 with an aldehyde group. In addition, these compounds also exhibited good inhibitory activity against the 3CL pro and the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), especially compound 18p (IC 50 = 0.034 μM, EC 50 = 0.29 μM). According to our previous work, these compounds have no reasons for concern regarding acute toxicity. Compared with AG7088 , compound 18p also exhibited good pharmacokinetic properties and more potent anticoronavirus activity, making it an excellent lead for further development.


  • Organizational Affiliation

    State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C protease183Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for B8YLW0 (Human enterovirus 71)
Explore B8YLW0 
Go to UniProtKB:  B8YLW0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8YLW0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FHR (Subject of Investigation/LOI)
Query on FHR

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide
C25 H32 N4 O4
HPKJGHVHQWJOOT-ZJOUEHCJSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.034α = 90
b = 95.034β = 90
c = 34.067γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release
  • Version 1.1: 2022-03-09
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary