4CB4

Structure of Influenza A H5N1 PB2 cap-binding domain with bound m7GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.170 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.126 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.128 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

New 7-Methyl-Guanosine Derivatives Targeting the Influenza Polymerase Pb2 CAP-Binding Domain

Pautus, S.Sehr, P.Lewis, J.Fortune, A.Wolkerstorfer, A.Szolar, O.Gulligay, D.Lunardi, T.Decout, J.L.Cusack, S.

(2013) J Med Chem 56: 8915

  • DOI: https://doi.org/10.1021/jm401369y
  • Primary Citation of Related Structures:  
    4CB4, 4CB5, 4CB6, 4CB7

  • PubMed Abstract: 

    The heterotrimeric influenza virus polymerase performs replication and transcription of viral RNA in the nucleus of infected cells. Transcription by "cap-snatching" requires that host-cell pre-mRNAs are bound via their 5' cap to the PB2 subunit. Thus, the PB2 cap-binding site is potentially a good target for new antiviral drugs that will directly inhibit viral replication. Docking studies using the structure of the PB2 cap-binding domain suggested that 7-alkylguanine derivatives substituted at position N-9 and N-2 could be good candidates. Four series of 7,9-di- and 2,7,9-trialkyl guanine derivatives were synthesized and evaluated by an AlphaScreen assay in competition with a biotinylated cap analogue. Three synthesized compounds display potent in vitro activity with IC50 values lower than 10 μM. High-resolution X-ray structures of three inhibitors in complex with the H5N1 PB2 cap-binding domain confirmed the binding mode and provide detailed information for further compound optimization.


  • Organizational Affiliation

    Département de Pharmacochimie Moléculaire, Université de Grenoble Alpes/CNRS, UMR 5063 , ICMG FR 2607, 470 rue de la Chimie, BP 53, F-38041 Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
POLYMERASE BASIC SUBUNIT 2167Influenza A virus (A/duck/Shantou/4610/2003(H5N1))Mutation(s): 0 
UniProt
Find proteins for Q2LG68 (Influenza A virus)
Explore Q2LG68 
Go to UniProtKB:  Q2LG68
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2LG68
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.170 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.126 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.128 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.48α = 90
b = 82.48β = 90
c = 55.24γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MGTClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2013-12-25
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description