9JO3 | pdb_00009jo3

Cryo-EM structure of human BKca channel-compound 10b complex

PDB DOI: https://doi.org/10.2210/pdb9JO3/pdb
EM Map EMD-61642: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes mpstruc

Deposited: 2024-09-24 Released: 2025-02-26
Deposition Author(s): Kim, S., Park, S., Lee, N.Y., Lee, E.Y., Lee, N., Roh, E.C., Kim, Y.G., Kim, H.J., Jin, M.S., Park, C.S., Kim, Y.C.
Funding Organization(s): Other government, National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 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

Discovery of Diphenyl Ether Derivatives as Novel BK Ca Channel Activators: Structure-Activity Relationship, Cryo-EM Complex Structures, and In Vivo Animal Studies.

Park, S.B., Lee, N.Y., Lee, E.Y., Kim, S., Lee, N., Roh, E.C., Kim, Y.G., Kim, H.J., Jin, M.S., Park, C.S., Kim, Y.C.

(2025) J Med Chem 68: 4259-4286

PubMed: 39947888 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.4c02008
Primary Citation of Related Structures:
9JO3, 9JO4

PubMed Abstract:
The BK _Ca channel, a large-conductance calcium-activated potassium channel, plays a crucial role in maintaining the homeostasis of the micturition cycle and airway-related functions. In this study, we optimized a novel BK _Ca channel activator, 4d , with a diphenyl ether structure identified from library screening. This led to the discovery of potent activators, 10b (EC ₅₀ = 0.12 μM, cell-based assay) and 51b , an orally bioavailable derivative. Compound 10b demonstrated potent in vivo efficacy in a spontaneous hypertensive rat (SHR) of urinary incontinence model, while compound 51b showed dose-dependent cough suppression efficacy with an ED ₅₀ of 11.8 mg/kg in a citric acid-induced cough model. Furthermore, we reported the cryo-electron microscopy (cryo-EM) structures of the BK _Ca channel in complex with 10b and 51b at resolutions of 2.8 and 3.4 Å. Based on structural analyses, we determined the binding sites and key interaction residues of 51b , which were validated via mutation studies.

Organizational Affiliation

School of Life Science, Gwangju Institute of Science and Technology, 123, Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea.

Macromolecule Content

Total Structure Weight: 513.89 kDa
Atom Count: 29,981
Modeled Residue Count: 3,674
Deposited Residue Count: 4,476
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-activated potassium channel subunit alpha-1	A, B, C, D	1,119	Homo sapiens	Mutation(s): 0 Gene Names: KCNMA1, KCNMA, SLO Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q12791 (Homo sapiens) Explore Q12791 Go to UniProtKB: Q12791
PHAROS: Q12791 GTEx: ENSG00000156113
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12791
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y01 Query on Y01 Download Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain MA [auth D] SDF format, chain M [auth A] SDF format, chain LA [auth D] SDF format, chain L [auth A] SDF format, chain KA [auth D] SDF format, chain JA [auth D] SDF format, chain EA [auth C] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain BA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C]	BA [auth C] CA [auth C] DA [auth C] EA [auth C] JA [auth D] BA [auth C], CA [auth C], DA [auth C], EA [auth C], JA [auth D], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], O [auth A], P [auth A], U [auth B], V [auth B], W [auth B]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
A1L4E Query on A1L4E Download Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain K [auth A] SDF format, chain IA [auth D] SDF format, chain AA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain K [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain K [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain AA [auth C]	AA [auth C], IA [auth D], K [auth A], T [auth B]	5-azanyl-2-[2,3,5,6-tetrakis(fluoranyl)-4-(trifluoromethyl)phenoxy]phenol C₁₃ H₆ F₇ N O₂ XNVYOMVIMRCYCP-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain IA [auth D] Focus chain K [auth A] Focus chain T [auth B] Interactions & Density Focus chain AA [auth C] Focus chain IA [auth D] Focus chain K [auth A] Focus chain T [auth B]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain HA [auth D] SDF format, chain GA [auth D] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain HA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain HA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] GA [auth D] HA [auth D] R [auth B] F [auth A], G [auth A], GA [auth D], HA [auth D], R [auth B], S [auth B], Y [auth C], Z [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
K (Subject of Investigation/LOI) Query on K Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], J [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain Q [auth B] SDF format, chain FA [auth D] SDF format, chain E [auth A] MOL2 format, chain X [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain FA [auth D] MOL2 format, chain E [auth A] mmCIF format, chain X [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain FA [auth D] mmCIF format, chain E [auth A]	E [auth A], FA [auth D], Q [auth B], X [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain FA [auth D] Focus chain Q [auth B] Focus chain X [auth C] Interactions & Density Focus chain E [auth A] Focus chain FA [auth D] Focus chain Q [auth B] Focus chain X [auth C]