9DFX | pdb_00009dfx

Cryo-EM structure of a SUR1/Kir6.2 ATP-sensitive potassium channel in the presence of Aekatperone in the closed conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

AI-based discovery and cryoEM structural elucidation of a K ATP channel pharmacochaperone.

Elsheikh, A.Driggers, C.M.Truong, H.H.Yang, Z.Allen, J.Henriksen, N.M.Walczewska-Szewc, K.Shyng, S.L.

(2025) Elife 13

  • DOI: https://doi.org/10.7554/eLife.103159
  • Primary Citation of Related Structures:  
    9DFX

  • PubMed Abstract: 

    Pancreatic K ATP channel trafficking defects underlie congenital hyperinsulinism (CHI) cases unresponsive to the K ATP channel opener diazoxide, the mainstay medical therapy for CHI. Current clinically used K ATP channel inhibitors have been shown to act as pharmacochaperones and restore surface expression of trafficking mutants; however, their therapeutic utility for K ATP trafficking-impaired CHI is hindered by high affinity binding, which limits functional recovery of rescued channels. Recent structural studies of K ATP channels employing cryo-electron microscopy (cryoEM) have revealed a promiscuous pocket where several known K ATP pharmacochaperones bind. The structural knowledge provides a framework for discovering K ATP channel pharmacochaperones with desired reversible inhibitory effects to permit functional recovery of rescued channels. Using an AI-based virtual screening technology AtomNet followed by functional validation, we identified a novel compound, termed Aekatperone, which exhibits chaperoning effects on K ATP channel trafficking mutations. Aekatperone reversibly inhibits K ATP channel activity with a half-maximal inhibitory concentration (IC 50 ) ~9 μM. Mutant channels rescued to the cell surface by Aekatperone showed functional recovery upon washout of the compound. CryoEM structure of K ATP bound to Aekatperone revealed distinct binding features compared to known high affinity inhibitor pharmacochaperones. Our findings unveil a K ATP pharmacochaperone enabling functional recovery of rescued channels as a promising therapeutic for CHI caused by K ATP trafficking defects.


  • Organizational Affiliation
    • Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-sensitive inward rectifier potassium channel 11A,
C [auth B],
D [auth C],
E [auth D]
390Rattus norvegicusMutation(s): 0 
Gene Names: Kcnj11
UniProt
Find proteins for P70673 (Rattus norvegicus)
Explore P70673 
Go to UniProtKB:  P70673
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP70673
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SUR1B [auth E]1,582Mesocricetus auratusMutation(s): 0 
UniProt
Find proteins for A0A1U7R319 (Mesocricetus auratus)
Explore A0A1U7R319 
Go to UniProtKB:  A0A1U7R319
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1U7R319
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
F [auth A],
J [auth E],
M [auth B],
N [auth C],
R [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
A1A4F (Subject of Investigation/LOI)
Query on A1A4F

Download Ideal Coordinates CCD File 
K [auth E]N-[3-(cyclohexylmethyl)-1H-pyrazol-5-yl]-2-[(1H-imidazol-1-yl)methyl]benzene-1-sulfonamide
C20 H25 N5 O2 S
ZPOQSBRRJBFXEB-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
L [auth E]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
K
Query on K

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
O [auth C]
P [auth C]
G [auth A],
H [auth A],
I [auth A],
O [auth C],
P [auth C],
Q [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK066485
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM129547

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Data collection, Database references