9RQK | pdb_00009rqk

COXSACKIE B3 2C PROTEIN IN COMPLEX WITH COMPOUND 53

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 
    0.223 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

New fluoxetine analogues as anti-enterovirus agents targeting 2C protein.

Khemiri, S., Faucher, M.O., Bourg, S., Attoumani-Madi, S., Yaacoub, C., Touret, F., Farag, M., Vitorino, M.F., Bonnet, P., Vanelle, P., Aci-Seche, S., Coutard, B., Barral, K.

(2026) Eur J Med Chem 306: 118621-118621

  • DOI: https://doi.org/10.1016/j.ejmech.2026.118621
  • Primary Citation Related Structures: 
    9RQK

  • PubMed Abstract: 

    There are currently no antiviral drugs available to treat or prevent life-threatening human non-poliovirus enterovirus infections, such as those caused by CV-B3, EV-A71 or EV-D68. Our aim is to develop novel inhibitors that target the non-structural ATPase/Helicase 2C protein, which is involved in the RNA replication process that is essential for enterovirus replication, among other functions. In this study, we describe the optimization of (S)-fluoxetine, a promising hit identified through drug repurposing that binds to an allosteric site on the CV-B3 2C ATPase domain. Our optimization process was guided by rational design, X-ray crystallographic structures, computational docking, and validation by enzyme and cell-based assays, leading to several new inhibitors, among which compound 53 (CV-B3 EC 50  = 0.5 μM and EV-D68 EC 50  = 0.4 μM), a novel anti-enterovirus with higher selectivity indexes than (S)-fluoxetine.

    • Organizational Affiliation: 
    • Aix Marseille Univ, CNRS, ICR, Marseille, France.

Macromolecule Content 

  • Total Structure Weight: 24.2 kDa 
  • Atom Count: 1,860 
  • Modeled Residue Count: 207 
  • Deposited Residue Count: 215 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
2C protein215Coxsackievirus B3Mutation(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 Q9E7C2 (Coxsackievirus B3)
Explore Q9E7C2 
Go to UniProtKB:  Q9E7C2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9E7C2
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.223 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.665α = 90
b = 55.724β = 90
c = 80γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-23-CE18-0023-01

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-18
    Type: Initial release