Co-crystal structure of Influenza A H3N2 PB2 (241-741) bound to VX-787

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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Structural basis for therapeutic inhibition of influenza A polymerase PB2 subunit.

Ma, X.Xie, L.Wartchow, C.Warne, R.Xu, Y.Rivkin, A.Tully, D.Shia, S.Uehara, K.Baldwin, D.M.Muiru, G.Zhong, W.Zaror, I.Bussiere, D.E.Leonard, V.H.J.

(2017) Sci Rep 7: 9385-9385

  • DOI: https://doi.org/10.1038/s41598-017-09538-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Influenza virus uses a unique mechanism to initiate viral transcription named cap-snatching. The PB2 subunit of the viral heterotrimeric RNA polymerase binds the cap structure of cellular pre-mRNA to promote its cleavage by the PA subunit. The resulting 11-13 capped oligomer is used by the PB1 polymerase subunit to initiate transcription of viral proteins. VX-787 is an inhibitor of the influenza A virus pre-mRNA cap-binding protein PB2. This clinical stage compound was shown to bind the minimal cap-binding domain of PB2 to inhibit the cap-snatching machinery. However, the binding of this molecule in the context of an extended form of the PB2 subunit has remained elusive. Here we generated a collection of PB2 truncations to identify a PB2 protein representative of its structure in the viral heterotrimeric protein. We present the crystal structure of VX-787 bound to a PB2 construct that recapitulates VX-787's biological antiviral activity in vitro. This co-structure reveals more extensive interactions than previously identified and provides insight into the observed resistance profile, affinity, binding kinetics, and conformational rearrangements induced by VX-787.

  • Organizational Affiliation

    Structural and Biophysical Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA. xiaolei.ma@novartis.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase basic protein 2510Influenza A virus (A/Udorn/307/1972(H3N2))Mutation(s): 0 
Gene Names: PB2
Find proteins for Q67296 (Influenza A virus (strain A/Udorn/307/1972 H3N2))
Explore Q67296 
Go to UniProtKB:  Q67296
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ67296
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 21G

Download Ideal Coordinates CCD File 
B [auth A](2S,3S)-3-[[5-fluoranyl-2-(5-fluoranyl-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid
C20 H19 F2 N5 O2
Query on PEG

Download Ideal Coordinates CCD File 
C4 H10 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.413α = 90
b = 56.752β = 111.23
c = 82.014γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary