7DNC | pdb_00007dnc

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 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.0 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 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.

Macromolecule Content 

  • Total Structure Weight: 20.58 kDa 
  • Atom Count: 1,570 
  • Modeled Residue Count: 179 
  • Deposited Residue Count: 183 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
A1L6N
(Subject of Investigation/LOI)

Query on A1L6N



Download:Ideal Coordinates CCD File
B [auth A]~{N}-[(2~{S})-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-3-phenyl-propan-2-yl]-1~{H}-indole-2-carboxamide
C25 H26 N4 O4
BRFDPJYHCJVJEP-ZJOUEHCJSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free:  0.187 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
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

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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
  • Version 2.0: 2024-12-18
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Other, Structure summary