[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleStructural Basis for Binding of Potassium-Competitive Acid Blockers to the Gastric Proton Pump.
Journal, issue, pagesJ Med Chem, Vol. 65, Issue 11, Page 7843-7853, Year 2022
Publish dateJun 9, 2022
AuthorsSaki Tanaka / Mikio Morita / Tatsuya Yamagishi / Hridya Valia Madapally / Kenichi Hayashida / Himanshu Khandelia / Christoph Gerle / Hideki Shigematsu / Atsunori Oshima / Kazuhiro Abe /
PubMed AbstractAs 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- ...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.
External linksJ Med Chem / PubMed:35604136
MethodsEM (single particle) / X-ray diffraction
Resolution2.76 - 3.5 Å
Structure data

32299

7w4a

EMDB-32299, PDB-7w4a:
Cryo-EM structure of the gastric proton pump complexed with revaprazan
Method: EM (single particle) / Resolution: 2.76 Å

PDB-7w47:
Crystal structure of the gastric proton pump complexed with tegoprazan
Method: X-RAY DIFFRACTION / Resolution: 3 Å

PDB-7w48:
Crystal structure of the gastric proton pump complexed with PF-03716556
Method: X-RAY DIFFRACTION / Resolution: 3.5 Å

PDB-7w49:
Crystal structure of the gastric proton pump complexed with soraprazan
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-RB:
RUBIDIUM ION

ChemComp-8BN:
Tegoprazan

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-HOH:
WATER

ChemComp-CE1:
O-DODECANYL OCTAETHYLENE GLYCOL

ChemComp-8BZ:
N-(2-hydroxyethyl)-N,2-dimethyl-8-[[(4R)-5-methyl-3,4-dihydro-2H-chromen-4-yl]amino]imidazo[1,2-a]pyridine-6-carboxamide

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

ChemComp-8CE:
Soraprazan

ChemComp-8CK:
N-(4-fluorophenyl)-4,5-dimethyl-6-[(1R)-1-methyl-3,4-dihydro-1H-isoquinolin-2-yl]pyrimidin-2-amine

ChemComp-NA:
Unknown entry

Source
  • sus scrofa (pig)
KeywordsHYDROLASE / Cation pump / P-type ATPase / gastric / proton pump / membrane protein / P-CAB

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more