8ZYQ

Cryo-EM Structure of pimozide-bound hERG Channel


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Improved higher resolution cryo-EM structures reveal the binding modes of hERG channel inhibitors.

Miyashita, Y.Moriya, T.Kato, T.Kawasaki, M.Yasuda, S.Adachi, N.Suzuki, K.Ogasawara, S.Saito, T.Senda, T.Murata, T.

(2024) Structure 32: 1926

  • DOI: https://doi.org/10.1016/j.str.2024.08.021
  • Primary Citation of Related Structures:  
    8ZYN, 8ZYO, 8ZYP, 8ZYQ

  • PubMed Abstract: 

    During drug discovery, it is crucial to exclude compounds with toxic effects. The human ether-à-go-go-related gene (hERG) channel is essential for maintaining cardiac repolarization and is a critical target in drug safety evaluation due to its role in drug-induced arrhythmias. Inhibition of the hERG channel can lead to severe cardiac issues, including Torsades de Pointes tachycardia. Understanding hERG inhibition mechanisms is essential to avoid these toxicities. Several structural studies have elucidated the interactions between inhibitors and hERG. However, orientation and resolution issues have so far limited detailed insights. Here, we used digitonin to analyze the apo state of hERG, which resolved orientation issues and improved the resolution. We determined the structure of hERG bound to astemizole, showing a clear map in the pore pathway. Using this strategy, we also analyzed the binding modes of E-4031 and pimozide. These insights into inhibitor interactions with hERG may aid safer drug design and enhance cardiac safety.


  • Organizational Affiliation

    Department of Developmental Biology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo, Chiba 260-8670, Japan; Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium voltage-gated channel subfamily H member 2
A, B, C, D
820Homo sapiensMutation(s): 0 
Gene Names: KCNH2ERGERG1HERG
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q12809 (Homo sapiens)
Explore Q12809 
Go to UniProtKB:  Q12809
PHAROS:  Q12809
GTEx:  ENSG00000055118 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12809
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1II (Subject of Investigation/LOI)
Query on 1II

Download Ideal Coordinates CCD File 
E [auth B]3-[1-[4,4-bis(4-fluorophenyl)butyl]piperidin-4-yl]-1~{H}-benzimidazol-2-one
C28 H29 F2 N3 O
YVUQSNJEYSNKRX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)Japan--
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-11-27
    Changes: Data collection, Database references