4KS4

Influenza Neuraminidase in complex with antiviral compound (3S,4R,5R)-4-(acetylamino)-3-{4-[(1R)-1-hydroxypropyl]-1H-1,2,3-triazol-1-yl}-5-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis for a class of nanomolar influenza A neuraminidase inhibitors.

Kerry, P.S.Mohan, S.Russell, R.J.Bance, N.Niikura, M.Pinto, B.M.

(2013) Sci Rep 3: 2871-2871

  • DOI: https://doi.org/10.1038/srep02871
  • Primary Citation of Related Structures:  
    4KS1, 4KS2, 4KS3, 4KS4, 4KS5

  • PubMed Abstract: 

    The influenza virus neuraminidase (NA) is essential for the virus life cycle. The rise of resistance mutations against current antiviral therapies has increased the need for the development of novel inhibitors. Recent efforts have targeted a cavity adjacent to the catalytic site (the 150-cavity) in addition to the primary catalytic subsite in order to increase specificity and reduce the likelihood of resistance. This study details structural and in vitro analyses of a class of inhibitors that bind uniquely in both subsites. Crystal structures of three inhibitors show occupation of the 150-cavity in two distinct and novel binding modes. We believe these are the first nanomolar inhibitors of NA to be characterized in this way. Furthermore, we show that one inhibitor, binding within the catalytic site, offers reduced susceptibility to known resistance mutations via increased flexibility of a pendant pentyloxy group and the ability to pivot about a strong hydrogen-bonding network.


  • Organizational Affiliation

    Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, KY16 9ST, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuraminidase390Influenza A virus (A/duck/Ukraine/1/1963(H3N8))Mutation(s): 0 
Gene Names: NA
UniProt
Find proteins for Q0A480 (Influenza A virus (strain A/Duck/Ukraine/1/1963 H3N8))
Explore Q0A480 
Go to UniProtKB:  Q0A480
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0A480
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1SN
Query on 1SN

Download Ideal Coordinates CCD File 
B [auth A](3S,4R,5R)-4-(acetylamino)-3-{4-[(1R)-1-hydroxypropyl]-1H-1,2,3-triazol-1-yl}-5-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid
C19 H30 N4 O5
GDVDNLLDXBKKJO-BSDSXHPESA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
1SN PDBBind:  4KS4 Ki: 72 (nM) from 1 assay(s)
Binding MOAD:  4KS4 Ki: 72 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.187 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.68α = 90
b = 90.68β = 90
c = 107.998γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-27
    Changes: Derived calculations