8F1C

Voltage-gated potassium channel Kv3.1 with novel positive modulator (9M)-9-{5-chloro-6-[(3,3-dimethyl-2,3-dihydro-1-benzofuran-4-yl)oxy]-4-methylpyridin-3-yl}-2-methyl-7,9-dihydro-8H-purin-8-one (compound 4)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Identification and structural and biophysical characterization of a positive modulator of human Kv3.1 channels.

Chen, Y.T.Hong, M.R.Zhang, X.J.Kostas, J.Li, Y.Kraus, R.L.Santarelli, V.P.Wang, D.Gomez-Llorente, Y.Brooun, A.Strickland, C.Soisson, S.M.Klein, D.J.Ginnetti, A.T.Marino, M.J.Stachel, S.J.Ishchenko, A.

(2023) Proc Natl Acad Sci U S A 120: e2220029120-e2220029120

  • DOI: https://doi.org/10.1073/pnas.2220029120
  • Primary Citation of Related Structures:  
    8F1C, 8F1D

  • PubMed Abstract: 

    Voltage-gated potassium channels (Kv) are tetrameric membrane proteins that provide a highly selective pathway for potassium ions (K + ) to diffuse across a hydrophobic cell membrane. These unique voltage-gated cation channels detect changes in membrane potential and, upon activation, help to return the depolarized cell to a resting state during the repolarization stage of each action potential. The Kv3 family of potassium channels is characterized by a high activation potential and rapid kinetics, which play a crucial role for the fast-spiking neuronal phenotype. Mutations in the Kv3.1 channel have been shown to have implications in various neurological diseases like epilepsy and Alzheimer's disease. Moreover, disruptions in neuronal circuitry involving Kv3.1 have been correlated with negative symptoms of schizophrenia. Here, we report the discovery of a novel positive modulator of Kv3.1, investigate its biophysical properties, and determine the cryo-EM structure of the compound in complex with Kv3.1. Structural analysis reveals the molecular determinants of positive modulation in Kv3.1 channels by this class of compounds and provides additional opportunities for rational drug design for the treatment of associated neurological disorders.


  • Organizational Affiliation

    Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium voltage-gated channel subfamily C member 1
A, B, C, D
552Homo sapiensMutation(s): 0 
Gene Names: KCNC1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P48547 (Homo sapiens)
Explore P48547 
Go to UniProtKB:  P48547
PHAROS:  P48547
GTEx:  ENSG00000129159 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48547
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV
Query on POV

Download Ideal Coordinates CCD File 
G [auth A],
N [auth B],
Q [auth C],
T [auth D]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
X9T (Subject of Investigation/LOI)
Query on X9T

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B],
P [auth C],
S [auth D]
(9M)-9-{5-chloro-6-[(3,3-dimethyl-2,3-dihydro-1-benzofuran-4-yl)oxy]-4-methylpyridin-3-yl}-2-methyl-7,9-dihydro-8H-purin-8-one
C22 H20 Cl N5 O3
MLPMJBILCUWBJI-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
O [auth C],
R [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
K [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Merck & Co.United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release