4M3M

Influenza Neuraminidase in complex with a stereomutated analogue of Oseltamivir carboxylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Synthesis, structure and inhibitory activity of a stereoisomer of oseltamivir carboxylate.

Sartori, A.Dell'amico, L.Battistini, L.Curti, C.Rivara, S.Pala, D.Kerry, P.S.Pelosi, G.Casiraghi, G.Rassu, G.Zanardi, F.

(2014) Org Biomol Chem 12: 1561-1569

  • DOI: 10.1039/c3ob42069h
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A stereodivergent plan is presented leading to all eight stereoisomers of oseltamivir carboxylate (OC). Key chemical manoeuvers are (1) a three-component vinylogous Mukaiyama-Mannich reaction, which sets the whole carbon skeleton and heteroatom subst ...

    A stereodivergent plan is presented leading to all eight stereoisomers of oseltamivir carboxylate (OC). Key chemical manoeuvers are (1) a three-component vinylogous Mukaiyama-Mannich reaction, which sets the whole carbon skeleton and heteroatom substituents, and (2) an intramolecular, silylative Mukaiyama aldol reaction, which creates the targeted carbocycle. The viability of the plan was demonstrated by the first total synthesis of 4-epi-oseltamivir carboxylate (6), accessed in 15 steps from glyceraldehyde, o-anisidine and pyrrole siloxydiene precursors. Compound 6 inhibits influenza A virus strains H1N1 and H3N2 at the μM level, about 150 000-fold less than the OC reference, testifying that the stereodisposition of the C4 acetamido function is key for enzyme recognition. Guided by in-depth structural evaluation including NMR solution studies, molecular mechanics simulations, docking analyses and X-ray crystallography, rationalization of the biological verdict was established.


    Organizational Affiliation

    Dipartimento di Farmacia, Università degli Studi di Parma, Parco Area delle Scienze 27A, I-43124 Parma, Italy. andrea.sartori@unipr.it franca.zanardi@unipr.it.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neuraminidase
A
390Influenza A virus (A/duck/Ukraine/1/1963(H3N8))Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
Find proteins for Q0A480 (Influenza A virus (strain A/Duck/Ukraine/1/1963 H3N8))
Go to UniProtKB:  Q0A480
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
22N
Query on 22N

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

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.832α = 90
b = 90.832β = 90
c = 111.987γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-08-06 
  • Released Date: 2014-02-12 
  • Deposition Author(s): Kerry, P.S.

Revision History 

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-03-26
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description