5WBX

Structural insights into the potency of SK/IK channel positive modulators


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural insights into the potency of SK channel positive modulators.

Nam, Y.W.Orfali, R.Liu, T.Yu, K.Cui, M.Wulff, H.Zhang, M.

(2017) Sci Rep 7: 17178-17178

  • DOI: 10.1038/s41598-017-16607-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Small-conductance Ca2+-activated K+ (SK) channels play essential roles in the regulation of cellular excitability and have been implicated in neurological and cardiovascular diseases through both animal model studies and human genetic association stu ...

    Small-conductance Ca2+-activated K+ (SK) channels play essential roles in the regulation of cellular excitability and have been implicated in neurological and cardiovascular diseases through both animal model studies and human genetic association studies. Over the past two decades, positive modulators of SK channels such as NS309 and 1-EBIO have been developed. Our previous structural studies have identified the binding pocket of 1-EBIO and NS309 that is located at the interface between the channel and calmodulin. In this study, we took advantage of four compounds with potencies varying over three orders of magnitude, including 1-EBIO, NS309, SKS-11 (6-bromo-5-methyl-1H-indole-2,3-dione-3-oxime) and SKS-14 (7-fluoro-3-(hydroxyimino)indolin-2-one). A combination of x-ray crystallographic, computational and electrophysiological approaches was utilized to investigate the interactions between the positive modulators and their binding pocket. A strong trend exists between the interaction energy of the compounds within their binding site calculated from the crystal structures, and the potency of these compounds in potentiating the SK2 channel current determined by electrophysiological recordings. Our results further reveal that the difference in potency of the positive modulators in potentiating SK2 channel activity may be attributed primarily to specific electrostatic interactions between the modulators and their binding pocket.


    Organizational Affiliation

    Department of Biomedical and Pharmaceutical Sciences & Structural Biology Research Center, Chapman University School of Pharmacy, Irvine, CA, 92618, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Small conductance calcium-activated potassium channel protein 2
B
95Homo sapiensMutation(s): 1 
Gene Names: KCNN2
Find proteins for Q9H2S1 (Homo sapiens)
Go to Gene View: KCNN2
Go to UniProtKB:  Q9H2S1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Calmodulin-1
R
146Homo sapiensMutation(s): 0 
Gene Names: CALM1 (CALM, CAM, CAM1)
Find proteins for P0DP23 (Homo sapiens)
Go to Gene View: CALM1
Go to UniProtKB:  P0DP23
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B, R
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
R
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
AJY
Query on AJY

Download SDF File 
Download CCD File 
R
(3Z)-6-bromo-3-(hydroxyimino)-5-methyl-1,3-dihydro-2H-indol-2-one
C9 H7 Br N2 O2
AGNBDYDENXJXFC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 77.328α = 90.00
b = 66.091β = 93.84
c = 65.435γ = 90.00
Software Package:
Software NamePurpose
XPREPdata reduction
REFMACrefinement
PHASERphasing
XPREPdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-06-29 
  • Released Date: 2017-12-20 
  • Deposition Author(s): Nam, Y.W., Zhang, M.

Funding OrganizationLocationGrant Number
American Heart AssociationUnited States13SDG16150007
National Ataxia FoundationUnited StatesYI-SCA

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Author supporting evidence
  • Version 1.2: 2018-03-07
    Type: Data collection
  • Version 1.3: 2018-04-18
    Type: Data collection