2LY0

Solution NMR structure of the influenza A virus S31N mutant (19-49) in presence of drug M2WJ332


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus.

Wang, J.Wu, Y.Ma, C.Fiorin, G.Wang, J.Pinto, L.H.Lamb, R.A.Klein, M.L.Degrado, W.F.

(2013) Proc.Natl.Acad.Sci.USA 110: 1315-1320

  • DOI: 10.1073/pnas.1216526110

  • PubMed Abstract: 
  • The influenza A virus M2 proton channel (A/M2) is the target of the antiviral drugs amantadine and rimantadine, whose use has been discontinued due to widespread drug resistance. Among the handful of drug-resistant mutants, S31N is found in more than ...

    The influenza A virus M2 proton channel (A/M2) is the target of the antiviral drugs amantadine and rimantadine, whose use has been discontinued due to widespread drug resistance. Among the handful of drug-resistant mutants, S31N is found in more than 95% of the currently circulating viruses and shows greatly decreased inhibition by amantadine. The discovery of inhibitors of S31N has been hampered by the limited size, polarity, and dynamic nature of its amantadine-binding site. Nevertheless, we have discovered small-molecule drugs that inhibit S31N with potencies greater than amantadine's potency against WT M2. Drug binding locks the protein into a well-defined conformation, and the NMR structure of the complex shows the drug bound in the homotetrameric channel, threaded between the side chains of Asn31. Unrestrained molecular dynamics simulations predicted the same binding site. This S31N inhibitor, like other potent M2 inhibitors, contains a charged ammonium group. The ammonium binds as a hydrate to one of three sites aligned along the central cavity that appear to be hotspots for inhibition. These sites might stabilize hydronium-like species formed as protons diffuse through the outer channel to the proton-shuttling residue His37 near the cytoplasmic end of the channel.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-9001, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Membrane ion channel M2
A, B, C, D
31Influenza A virus (A/Chiba/5/71(H3N2))Gene Names: M
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
M2 proton channel (AM2)
Find proteins for Q6XT21 (Influenza A virus (A/Chiba/5/71(H3N2)))
Go to UniProtKB:  Q6XT21
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A2Y
Query on A2Y

Download SDF File 
Download CCD File 
A
(3S,5S,7S)-N-{[5-(thiophen-2-yl)-1,2-oxazol-3-yl]methyl}tricyclo[3.3.1.1~3,7~]decan-1-aminium
C18 H23 N2 O S
PBZWFIHUWUZQDJ-WXZYKRPKSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
A2YIC50: 16000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 2LY0 Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-09
    Type: Initial release
  • Version 1.1: 2013-01-23
    Type: Database references
  • Version 1.2: 2013-02-06
    Type: Database references