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

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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 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.

Macromolecule Content 

  • Total Structure Weight: 113.87 kDa 
  • Atom Count: 6,845 
  • Modeled Residue Count: 855 
  • Deposited Residue Count: 996 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 S5G2J2 (Influenza A virus)
Explore S5G2J2 
Go to UniProtKB:  S5G2J2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS5G2J2
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

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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