6CQ8

K2P2.1(TREK-1):ML335 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

K2P2.1 (TREK-1)-activator complexes reveal a cryptic selectivity filter binding site.

Lolicato, M.Arrigoni, C.Mori, T.Sekioka, Y.Bryant, C.Clark, K.A.Minor, D.L.

(2017) Nature 547: 364-368

  • DOI: 10.1038/nature22988
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Polymodal thermo- and mechanosensitive two-pore domain potassium (K <sub>2P </sub>) channels of the TREK subfamily generate 'leak' currents that regulate neuronal excitability, respond to lipids, temperature and mechanical stretch, and influence pain ...

    Polymodal thermo- and mechanosensitive two-pore domain potassium (K 2P ) channels of the TREK subfamily generate 'leak' currents that regulate neuronal excitability, respond to lipids, temperature and mechanical stretch, and influence pain, temperature perception and anaesthetic responses. These dimeric voltage-gated ion channel (VGIC) superfamily members have a unique topology comprising two pore-forming regions per subunit. In contrast to other potassium channels, K 2P channels use a selectivity filter 'C-type' gate as the principal gating site. Despite recent advances, poor pharmacological profiles of K 2P channels limit mechanistic and biological studies. Here we describe a class of small-molecule TREK activators that directly stimulate the C-type gate by acting as molecular wedges that restrict interdomain interface movement behind the selectivity filter. Structures of K 2P 2.1 (also known as TREK-1) alone and with two selective K 2P 2.1 (TREK-1) and K 2P 10.1 (TREK-2) activators-an N-aryl-sulfonamide, ML335, and a thiophene-carboxamide, ML402-define a cryptic binding pocket unlike other ion channel small-molecule binding sites and, together with functional studies, identify a cation-π interaction that controls selectivity. Together, our data reveal a druggable K 2P site that stabilizes the C-type gate 'leak mode' and provide direct evidence for K 2P selectivity filter gating.


    Organizational Affiliation

    California Institute for Quantitative Biomedical Research, University of California, San Francisco, California 941158-9001, USA.,Ono Pharmaceutical Co. Ltd, Mishima-Gun, Osaka 618-8585, Japan.,Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, California 941158-9001, USA.,Small Molecule Discovery Center, University of California, San Francisco, California 93858-2330, USA.,Departments of Biochemistry and Biophysics, and Cellular and Molecular Pharmacology, University of California, San Francisco, California 941158-9001, USA.,Cardiovascular Research Institute, University of California, San Francisco, California 941158-9001, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Potassium channel subfamily K member 2
A, B
312Mus musculusMutation(s): 15 
Gene Names: Kcnk2
Find proteins for P97438 (Mus musculus)
Go to UniProtKB:  P97438
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
R16
Query on R16

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Download CCD File 
A, B
HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
 Ligand Interaction
16C
Query on 16C

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Download CCD File 
A
N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE
C16-CERAMIDE, N-PALMITOYL-D-ERYTHRO-SPHINGOSINE, (2S,3R,4E)-2-PALMITOYLAMINOOCTADEC-4-ENE-1,3-DIOL, (2S,3R,4E)-2-PALMITOYLAMINO-1,3-OCTADEC-4-ENEDIOL
C34 H67 N O3
YDNKGFDKKRUKPY-TURZORIXSA-N
 Ligand Interaction
Q6F
Query on Q6F

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Download CCD File 
A, B
N-[(2,4-dichlorophenyl)methyl]-4-[(methylsulfonyl)amino]benzamide
C15 H14 Cl2 N2 O3 S
RDFIQTZRJRVFHK-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

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Download CCD File 
B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.257 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.074α = 90.00
b = 119.386β = 90.00
c = 128.179γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata processing
PHASERphasing
PHENIXrefinement
Cootmodel building
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United States--
American Heart AssociationUnited States--

Revision History 

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Author supporting evidence, Data collection
  • Version 1.2: 2019-11-06
    Type: Author supporting evidence, Data collection, Database references
  • Version 1.3: 2019-11-27
    Type: Author supporting evidence