4KS1

Influenza neuraminidase in complex with antiviral compound (3S,4R,5R)-4-(acetylamino)-3-amino-5-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1038/srep02871
  • Primary Citation of Related Structures:  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 a ...

    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: 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2H8
Query on 2H8

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Download CCD File 
A
(3S,4R,5R)-4-(acetylamino)-3-amino-5-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid
C14 H24 N2 O4
OTOZLTSLQBBOIB-YNEHKIRRSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2H8Kd: 1.5 nM BINDINGMOAD
2H8Ki: 1.5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.153 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 90.253α = 90.00
b = 90.253β = 90.00
c = 94.116γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-30
    Type: Initial release