9OUC | pdb_00009ouc

Influenza A Virus Nucleoprotein(8-498)NP complex with 5-(4-(morpholinomethyl)phenyl)-2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carboxamide (Compound 3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 
    0.307 (Depositor), 0.305 (DCC) 
  • R-Value Work: 
    0.266 (Depositor), 0.257 (DCC) 
  • R-Value Observed: 
    0.268 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery and Optimization of a Novel Series of Influenza A Virus Replication Inhibitors Targeting the Nucleoprotein Protein-Protein Interaction.

Taft, B.R.Hesse, M.J.Mamo, M.Bussiere, D.E.Huang, R.Lee, P.S.Wedel, L.Growcott, E.Wolff, K.C.Kuhen, K.Abend, J.Wong, K.A.Ganem, D.Leonard, V.H.J.Tully, D.C.

(2025) J Med Chem 68: 16349-16370

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01233
  • Primary Citation of Related Structures:  
    9OTW, 9OUC, 9OUG

  • PubMed Abstract: 

    Influenza A virus (IAV) is a negative-sense, single-stranded RNA virus that causes seasonal epidemic respiratory infections, with novel subtypes of IAV historically able to lead to pandemics that spread on a global scale. We conducted a phenotypic high-throughput screen (HTS) that identified compound 1 as a singleton hit. Resistant viral mutants generated against analog 2 revealed mutations in the nucleoprotein (NP). An X-ray cocrystal structure of NP in complex with compound 3 helped define the novel mechanism of action as disruption of the NP-NP protein-protein interaction (PPI), leading to inhibition of NP oligomerization and blocking viral replication. Medicinal chemistry optimization efforts resulted in the identification of compound 20 (VNT-101) as a potent IAV inhibitor with low nM activity across multiple subtypes. Compound 20 has attractive DMPK and physicochemical properties, and demonstrated robust antiviral activity in rodent models of influenza infection, leading to successful completion of IND-enabling safety studies.


  • Organizational Affiliation
    • Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoprotein
A, B
498Influenza A virus (A/(Puerto Rico/8/1934-Korea/426/1968)(H2N2))Mutation(s): 0 
Gene Names: NP
UniProt
Find proteins for P03466 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Explore P03466 
Go to UniProtKB:  P03466
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03466
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free:  0.307 (Depositor), 0.305 (DCC) 
  • R-Value Work:  0.266 (Depositor), 0.257 (DCC) 
  • R-Value Observed: 0.268 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.968α = 90
b = 96.861β = 90
c = 285.255γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Adxvdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2025-08-06 
  • Deposition Author(s): Mamo, M.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-08-20
    Changes: Database references