5WC5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1038/s41598-017-16607-8
  • Primary Citation of Related Structures:  
    5WBX, 5WC5

  • PubMed Abstract: 

    Small-conductance Ca 2+ -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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Small conductance calcium-activated potassium channel protein 2A [auth B]95Homo sapiensMutation(s): 1 
Gene Names: KCNN2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2S1 (Homo sapiens)
Explore Q9H2S1 
Go to UniProtKB:  Q9H2S1
PHAROS:  Q9H2S1
GTEx:  ENSG00000080709 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H2S1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-1B [auth R]146Homo sapiensMutation(s): 0 
Gene Names: CALM1CALMCAMCAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
PHAROS:  P0DP23
GTEx:  ENSG00000198668 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP23
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AJV
Query on AJV

Download Ideal Coordinates CCD File 
L [auth R]7-fluoro-3-(hydroxyamino)-2H-indol-2-one
C8 H5 F N2 O2
NTVMSTRPGVBVRX-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth B]
D [auth B]
E [auth B]
F [auth B]
J [auth R]
C [auth B],
D [auth B],
E [auth B],
F [auth B],
J [auth R],
K [auth R]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth R],
I [auth R]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.994α = 90
b = 66.015β = 93.76
c = 65.298γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XPREPdata scaling
PDB_EXTRACTdata extraction
XPREPdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Author supporting evidence
  • Version 1.2: 2018-03-07
    Changes: Data collection
  • Version 1.3: 2018-04-18
    Changes: Data collection
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations