9VVO

cryo-EM structure of gastric proton pump bound to YK01

This is a non-PDB format compatible entry.

Summary for 9VVO

• Entry DOI: 10.2210/pdb9vvo/pdb
• EMDB information: 65385
• Descriptor: Sodium/potassium-transporting ATPase subunit alpha, Potassium-transporting ATPase subunit beta, 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, ... (8 entities in total)
• Functional Keywords: p-type atpase, transporters, gastric, p-cabs, proton pump, membrane protein
• Biological source: Sus scrofa (pig); More
• Total number of polymer chains: 2
• Total formula weight: 144564.52

Authors

Saito, H.,Abe, K. (deposition date: 2025-07-16, release date: 2026-01-14, Last modification date: 2026-02-18)

Primary citation

Umekubo, N.,Hashizume, A.,Saito, H.,Kato, S.,Kanai, C.,Gopalasingam, C.C.,Gerle, C.,Shigematsu, H.,Yoshimori, A.,Abe, K.,Yokoshima, S.
Design, synthesis, and structural analysis of an inhibitor of the gastric proton pump with a diaza-tricyclic skeleton.
Org.Biomol.Chem., 24:1000-1005, 2026

PubMed Abstract: The development of potent K-competitive acid blockers (P-CABs) as inhibitors of acid gastric secretion attracts much research attention. In this study, the structure-guided design and enantioselective synthesis of P-CABs yielded a diaza-tricyclic compound with moderate inhibitory activity against the gastric proton pump. The eutomer was experimentally confirmed, consistent with pharmacophore predictions, and its binding mode to the gastric proton pump was elucidated cryo-electron microscopy.

PubMed: 41536160
DOI: 10.1039/d5ob01828e

Experimental method

ELECTRON MICROSCOPY (2.66 Å)