7W4A image
Entry Detail
PDB ID:
7W4A
EMDB ID:
Keywords:
Title:
Cryo-EM structure of the gastric proton pump complexed with revaprazan
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2021-11-26
Release Date:
2022-03-02
Method Details:
Experimental Method:
Resolution:
2.76 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Potassium-transporting ATPase alpha chain 1
Chain IDs:A
Chain Length:1034
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Potassium-transporting ATPase subunit beta
Chain IDs:B
Chain Length:290
Number of Molecules:1
Biological Source:Sus scrofa
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
BFD A ASP modified residue
Primary Citation
Structural Basis for Binding of Potassium-Competitive Acid Blockers to the Gastric Proton Pump.
J.Med.Chem. 65 7843 7853 (2022)
PMID: 35604136 DOI: 10.1021/acs.jmedchem.2c00338

Abstact

As specific inhibitors of the gastric proton pump, responsible for gastric acidification, K+-competitive acid blockers (P-CABs) have recently been utilized in the clinical treatment of gastric acid-related diseases in Asia. However, as these compounds have been developed based on phenotypic screening, their detailed binding poses are unknown. We show crystal and cryo-EM structures of the gastric proton pump in complex with four different P-CABs, tegoprazan, soraprazan, PF-03716556 and revaprazan, at resolutions reaching 2.8 Å. The structures describe molecular details of their interactions and are supported by functional analyses of mutations and molecular dynamics simulations. We reveal that revaprazan has a novel binding mode in which its tetrahydroisoquinoline moiety binds deep in the cation transport conduit. The mechanism of action of these P-CABs can now be evaluated at the molecular level, which will facilitate the rational development and improvement of currently available P-CABs to provide better treatment of acid-related gastrointestinal diseases.

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Primary Citation of related structures