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 

wwPDB Validation 3D Report Full Report


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: 10.1002/anie.201308142
  • Primary Citation of Related Structures:  4MJU

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neuraminidase
A
390Influenza A virus (strain A/Duck/Ukraine/1/1963 H3N8)Gene Names: NA
EC: 3.2.1.18
Find proteins for Q07599 (Influenza A virus (strain A/Duck/Ukraine/1/1963 H3N8))
Go to UniProtKB:  Q07599
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
27V
Query on 27V

Download SDF File 
Download CCD File 
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
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.200 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 90.744α = 90.00
b = 90.744β = 90.00
c = 112.002γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-09-04 
  • Released Date: 2014-01-15 
  • Deposition Author(s): Kerry, P.S.

Revision History 

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