4MJV

Influenza Neuraminidase in complex with a novel antiviral compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Serendipitous discovery of a potent influenza virus a neuraminidase inhibitor.

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

(2014) Angew Chem Int Ed Engl 53: 1076-1080

  • DOI: https://doi.org/10.1002/anie.201308142
  • Primary Citation of Related Structures:  
    4MJU, 4MJV

  • PubMed Abstract: 

    We have previously reported a potent neuraminidase inhibitor that comprises a carbocyclic analogue of zanamivir in which the hydrophilic glycerol side chain is replaced by the hydrophobic 3-pentyloxy group of oseltamivir. This hybrid inhibitor showed excellent inhibitory properties in the neuraminidase inhibition assay (Ki =0.46 nM; Ki (zanamivir) =0.16 nM) and in the viral replication inhibition assay in cell culture at 10(-8)  M. As part of this lead optimization, we now report a novel spirolactam that shows comparable inhibitory activity in the cell culture assay to that of our lead compound at 10(-7)  M. The compound was discovered serendipitously during the attempted synthesis of the isothiourea derivative of the original candidate. The X-ray crystal structure of the spirolactam in complex with the N8 subtype neuraminidase offers insight into the mode of inhibition.


  • Organizational Affiliation

    Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A1S6 (Canada) http://www.sfu.ca/chemistry/groups/pinto/


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 
EC: 3.2.1.18
UniProt
Find proteins for Q07599 (Influenza A virus (strain A/Duck/Ukraine/1/1963 H3N8))
Explore Q07599 
Go to UniProtKB:  Q07599
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07599
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
27V
Query on 27V

Download Ideal Coordinates CCD File 
B [auth A](2E,5S,9R,10S)-10-(acetylamino)-2-imino-4-oxo-9-(pentan-3-yloxy)-1-thia-3-azaspiro[4.5]dec-6-ene-7-carboxylic acid
C16 H23 N3 O5 S
YPLGHUGDNRYXJS-WQGACYEGSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.208 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.744α = 90
b = 90.744β = 90
c = 112.002γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2014-01-15 
  • Deposition Author(s): Kerry, P.S.

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-02-19
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description