6BKL

Influenza A M2 transmembrane domain bound to rimantadine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Inhibitors of the M2 Proton Channel Engage and Disrupt Transmembrane Networks of Hydrogen-Bonded Waters.

Thomaston, J.L.Polizzi, N.F.Konstantinidi, A.Wang, J.Kolocouris, A.DeGrado, W.F.

(2018) J Am Chem Soc 140: 15219-15226

  • DOI: 10.1021/jacs.8b06741
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Water-mediated interactions play key roles in drug binding. In protein sites with sparse polar functionality, a small-molecule approach is often viewed as insufficient to achieve high affinity and specificity. Here we show that small molecules can en ...

    Water-mediated interactions play key roles in drug binding. In protein sites with sparse polar functionality, a small-molecule approach is often viewed as insufficient to achieve high affinity and specificity. Here we show that small molecules can enable potent inhibition by targeting key waters. The M2 proton channel of influenza A is the target of the antiviral drugs amantadine and rimantadine. Structural studies of drug binding to the channel using X-ray crystallography have been limited because of the challenging nature of the target, with the one previously solved crystal structure limited to 3.5 Å resolution. Here we describe crystal structures of amantadine bound to M2 in the Inward closed conformation (2.00 Å), rimantadine bound to M2 in both the Inward closed (2.00 Å) and Inward open (2.25 Å) conformations, and a spiro-adamantyl amine inhibitor bound to M2 in the Inward closed conformation (2.63 Å). These X-ray crystal structures of the M2 proton channel with bound inhibitors reveal that ammonium groups bind to water-lined sites that are hypothesized to stabilize transient hydronium ions formed in the proton-conduction mechanism. Furthermore, the ammonium and adamantyl groups of the adamantyl-amine class of drugs are free to rotate in the channel, minimizing the entropic cost of binding. These drug-bound complexes provide the first high-resolution structures of drugs that interact with and disrupt networks of hydrogen-bonded waters that are widely utilized throughout nature to facilitate proton diffusion within proteins.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Matrix protein 2
A, B, C, D, E, F, G, H
27Influenza A virusMutation(s): 2 
Find proteins for Q9Q0L9 (Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd))
Go to UniProtKB:  Q9Q0L9
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EU7
Query on EU7

Download CCD File 
C, G
(1S)-1-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]decan-1-yl]ethan-1-amine
C12 H21 N
UBCHPRBFMUDMNC-SVNGYHJRSA-N
 Ligand Interaction
RIM
Query on RIM

Download CCD File 
D, F
RIMANTADINE
C12 H21 N
UBCHPRBFMUDMNC-RMPHRYRLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.46α = 90
b = 47.84β = 96.76
c = 48.53γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM056423

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence