4H52

Wild-type influenza N2 neuraminidase covalent complex with 3-fluoro-Neu5Ac


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Influenza neuraminidase operates via a nucleophilic mechanism and can be targeted by covalent inhibitors

Vavricka, C.J.Liu, Y.Kiyota, H.Sriwilaijaroen, N.Qi, J.Tanaka, K.Wu, Y.Li, Q.Li, Y.Yan, J.Suzuki, Y.Gao, G.F.

(2013) Nat Commun 4: 1491-1491

  • DOI: 10.1038/ncomms2487
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Development of novel influenza neuraminidase inhibitors is critical for preparedness against influenza outbreaks. Knowledge of the neuraminidase enzymatic mechanism and transition-state analogue, 2-deoxy-2,3-didehydro-N-acetylneuraminic acid, contrib ...

    Development of novel influenza neuraminidase inhibitors is critical for preparedness against influenza outbreaks. Knowledge of the neuraminidase enzymatic mechanism and transition-state analogue, 2-deoxy-2,3-didehydro-N-acetylneuraminic acid, contributed to the development of the first generation anti-neuraminidase drugs, zanamivir and oseltamivir. However, lack of evidence regarding influenza neuraminidase key catalytic residues has limited strategies for novel neuraminidase inhibitor design. Here, we confirm that influenza neuraminidase conserved Tyr406 is the key catalytic residue that may function as a nucleophile; thus, mechanism-based covalent inhibition of influenza neuraminidase was conceived. Crystallographic studies reveal that 2α,3ax-difluoro-N-acetylneuraminic acid forms a covalent bond with influenza neuraminidase Tyr406 and the compound was found to possess potent anti-influenza activity against both influenza A and B viruses. Our results address many unanswered questions about the influenza neuraminidase catalytic mechanism and demonstrate that covalent inhibition of influenza neuraminidase is a promising and novel strategy for the development of next-generation influenza drugs.


    Organizational Affiliation

    Research Network of Immunity and Health, Beijing Institutes of Life Science, Beijing 100101, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neuraminidase
A, B
388Influenza A virusMutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
Find proteins for Q194T1 (Influenza A virus)
Go to UniProtKB:  Q194T1
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FSI
Query on FSI

Download CCD File 
A, B
5-(acetylamino)-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid
C11 H18 F N O9
ALJLGESFXXDPKH-RISWTRDCSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.698α = 90
b = 139.704β = 90
c = 140.07γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2013-02-27
    Changes: Structure summary
  • Version 1.2: 2013-07-31
    Changes: Database references, Derived calculations