9IBY | pdb_00009iby

Crystal structure of Zika Virus NS2B-NS3 protease in complex with compound 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 
    0.236 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.195 (DCC) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

An allosteric inhibitor of the Zika virus NS2B-NS3 protease with oral efficacy in mouse models.

Ontoria, J.M.Torrente, E.Missineo, A.Alli, C.Graziani, R.Conti, S.Bisbocci, M.Quotadamo, A.Ferrigno, F.Corio, A.Ievoli, G.Bencheva, L.Amaudrut, J.Vasile, S.Beghetto, E.Paolini, C.Alaimo, N.Veneziano, M.Nibbio, M.Orsale, M.V.Proto, G.Colaceci, F.Orsatti, L.Pucci, V.Di Fabio, R.Tomei, L.Montalbetti, C.Bresciani, A.Toniatti, C.Paonessa, G.

(2026) Nat Commun 17: 1439-1439

  • DOI: https://doi.org/10.1038/s41467-026-68943-x
  • Primary Citation of Related Structures:  
    9IBY, 9TPG

  • PubMed Abstract: 

    The mosquito-transmitted Zika virus (ZIKV) poses a global health threat, with no approved antiviral drugs or vaccines currently available. Here, we report the discovery of a series of ZIKV NS3 protease inhibitors identified through phenotypic high-throughput screening (HTS) using a ZIKV replicon-based cellular assay, and the subsequent selection of resistant mutants. These inhibitors, characterized by the presence of an N-acylsydnone imine group, bind to a previously undescribed allosteric pocket of the protease, locking the enzyme into a catalytically inactive conformation. We describe the characterization of IRBM-Z-1, our initial allosteric hit and IRBM-Z-2, a potent inhibitor of ZIKV infectivity and other orthoflavivirus proteases with a favourable in vitro and in vivo ADME profile, resulting in oral efficacy against ZIKV infection in mouse models, with potential as a prophylactic agent for human use.


  • Organizational Affiliation
    • Department of Drug Discovery, IRBM S.p.A., Pomezia, Italy. j.ontoria@irbm.com.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyprotein
A, B
230Zika virusMutation(s): 0 
UniProt
Find proteins for A0A140DLX4 (Zika virus)
Explore A0A140DLX4 
Go to UniProtKB:  A0A140DLX4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140DLX4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free:  0.236 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.195 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.793α = 90
b = 57.472β = 96.406
c = 72.447γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release
  • Version 1.1: 2026-02-25
    Changes: Database references