3RO5

Crystal structure of influenza A virus nucleoprotein with ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Inhibition of influenza virus replication via small molecules that induce the formation of higher-order nucleoprotein oligomers.

Gerritz, S.W.Cianci, C.Kim, S.Pearce, B.C.Deminie, C.Discotto, L.McAuliffe, B.Minassian, B.F.Shi, S.Zhu, S.Zhai, W.Pendri, A.Li, G.Poss, M.A.Edavettal, S.McDonnell, P.A.Lewis, H.A.Maskos, K.Mortl, M.Kiefersauer, R.Steinbacher, S.Baldwin, E.T.Metzler, W.Bryson, J.Healy, M.D.Philip, T.Zoeckler, M.Schartman, R.Sinz, M.Leyva-Grado, V.H.Hoffmann, H.H.Langley, D.R.Meanwell, N.A.Krystal, M.

(2011) Proc Natl Acad Sci U S A 108: 15366-15371

  • DOI: https://doi.org/10.1073/pnas.1107906108
  • Primary Citation of Related Structures:  
    3RO5

  • PubMed Abstract: 

    Influenza nucleoprotein (NP) plays multiple roles in the virus life cycle, including an essential function in viral replication as an integral component of the ribonucleoprotein complex, associating with viral RNA and polymerase within the viral core. The multifunctional nature of NP makes it an attractive target for antiviral intervention, and inhibitors targeting this protein have recently been reported. In a parallel effort, we discovered a structurally similar series of influenza replication inhibitors and show that they interfere with NP-dependent processes via formation of higher-order NP oligomers. Support for this unique mechanism is provided by site-directed mutagenesis studies, biophysical characterization of the oligomeric ligand:NP complex, and an X-ray cocrystal structure of an NP dimer of trimers (or hexamer) comprising three NP_A:NP_B dimeric subunits. Each NP_A:NP_B dimeric subunit contains two ligands that bridge two composite, protein-spanning binding sites in an antiparallel orientation to form a stable quaternary complex. Optimization of the initial screening hit produced an analog that protects mice from influenza-induced weight loss and mortality by reducing viral titers to undetectable levels throughout the course of treatment.


  • Organizational Affiliation

    Bristol-Myers Squibb Research and Development, Wallingford, CT 06492, USA. samuel.gerritz@bms.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleocapsid protein
A, B
499Influenza A virus (A/Wilson-Smith/1933(H1N1))Mutation(s): 0 
Gene Names: NP
UniProt
Find proteins for Q1K9H2 (Influenza A virus (strain A/Wilson-Smith/1933 H1N1))
Explore Q1K9H2 
Go to UniProtKB:  Q1K9H2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1K9H2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LGH
Query on LGH

Download Ideal Coordinates CCD File 
C [auth B],
D [auth B]
[4-(2-chloro-4-nitrophenyl)piperazin-1-yl][3-(2-methoxyphenyl)-5-methyl-1,2-oxazol-4-yl]methanone
C22 H21 Cl N4 O5
OQYUKAFYGKRXTK-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.2α = 90
b = 146.2β = 90
c = 146.2γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-14
    Type: Initial release
  • Version 1.1: 2011-09-21
    Changes: Database references
  • Version 1.2: 2011-09-28
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations