6S5V | pdb_00006s5v

Crystal structure of the Cap-Midlink region of the H5N1 Influenza A virus polymerase in complex with a Cap-domain binding analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.165 (Depositor), 0.169 (DCC) 
  • R-Value Work: 
    0.148 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 
    0.149 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6S5V

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Design, Synthesis, and Biological Evaluation of Novel Indoles Targeting the Influenza PB2 Cap Binding Region.

McGowan, D.C.Balemans, W.Embrechts, W.Motte, M.Keown, J.R.Buyck, C.Corbera, J.Funes, M.Moreno, L.Cooymans, L.Tahri, A.Eymard, J.Stoops, B.Strijbos, R.Van den Berg, J.Fodor, E.Grimes, J.M.Koul, A.Jonckers, T.H.M.Raboisson, P.Guillemont, J.

(2019) J Med Chem 62: 9680-9690

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01091
  • Primary Citation Related Structures: 
    6S5V

  • PubMed Abstract: 

    In the search for novel influenza inhibitors we evaluated 7-fluoro-substituted indoles as bioisosteric replacements for the 7-azaindole scaffold of Pimodivir, a PB2 (polymerase basic protein 2) inhibitor currently in clinical development. Specifically, a 5,7-difluoroindole derivative 11a was identified as a potent and metabolically stable influenza inhibitor. 11a demonstrated a favorable oral pharmacokinetic profile and in vivo efficacy in mice. In addition, it was found that 11a was not at risk of metabolism via aldehyde oxidase, an advantage over previously described inhibitors of this class. The crystal structure of 11a bound to influenza A PB2 cap region is disclosed here and deposited to the PDB.


  • Organizational Affiliation
    • Janssen Pharmaceutica, N.V. , Turnhoutseweg 30 , 2340 Beerse , Belgium.

Macromolecule Content 

  • Total Structure Weight: 70.07 kDa 
  • Atom Count: 5,006 
  • Modeled Residue Count: 550 
  • Deposited Residue Count: 608 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Polymerase basic protein 2A [auth AAAA],
B [auth ABAA]
304Influenza A virus (A/duck/Fujian/13/2002(H5N1))Mutation(s): 0 
Gene Names: PB2
UniProt
Find proteins for Q6E3N3 (Influenza A virus)
Explore Q6E3N3 
Go to UniProtKB:  Q6E3N3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6E3N3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KWN
(Subject of Investigation/LOI)

Query on KWN



Download:Ideal Coordinates CCD File
C [auth AAAA],
F [auth ABAA],
H [auth ABAA]
(1~{S},2~{S},3~{S},6~{R})-2-[[2-[5,7-bis(fluoranyl)-1~{H}-indol-3-yl]-5-fluoranyl-pyrimidin-4-yl]amino]-3,6-dimethyl-cyclohexane-1-carboxylic acid
C21 H21 F3 N4 O2
HENNGHMYDSBUNC-SBJSHCRGSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth AAAA],
E [auth AAAA],
G [auth ABAA]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
I [auth ABAA]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.165 (Depositor), 0.169 (DCC) 
  • R-Value Work:  0.148 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 0.149 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.703α = 90
b = 105.703β = 90
c = 140.657γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom200835/Z/16/Z
Medical Research Council (United Kingdom)United KingdomMR/R009945/1
Medical Research Council (United Kingdom)United KingdomMR/K000241/1

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references