4CB5

Structure of Influenza A H5N1 PB2 cap-binding domain with bound cap analogue (compound 8f)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.127 

wwPDB Validation 3D Report Full Report


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: 10.1021/jm401369y
  • Primary Citation of Related Structures:  

  • 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 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POLYMERASE BASIC SUBUNIT 2
A
167Influenza A virusMutation(s): 0 
Gene Names: PB2
Find proteins for Q2LG68 (Influenza A virus)
Go to UniProtKB:  Q2LG68
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
93G
Query on 93G

Download SDF File 
Download CCD File 
A
9-N-(3-CARBOXY-4-HYDROXYPHENYL)KETOMETHYL-7-N-METHYLGUANINE
C15 H15 N6 O4
RSZNPUKMOKHZOH-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
93GKd: 13000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.127 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 82.170α = 90.00
b = 82.170β = 90.00
c = 54.840γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2013-12-25
    Type: Database references
  • Version 1.2: 2018-04-11
    Type: Data collection, Source and taxonomy