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Ligand docking in the gastric H+/K+-ATPase: homology modeling of reversible inhibitor binding sites.
| Content Provider | Semantic Scholar |
|---|---|
| Author | Kim, Chang Gon Watts, Jude A. Watts, Anthony |
| Copyright Year | 2005 |
| Abstract | Using the recent high-resolution X-ray structures determined for the Ca2+-ATPase, we have generated two homology models of the gastric H+/K+-ATPase reflecting the E1 and E2 conformations adopted by P-type ATPases in their catalytic cycle. In regimes where the in situ solid-state NMR-determined structure for 1,2,3-trimethyl-8-(pentafluorophenylmethoxy)imidazo[1,2-a]pyridinium iodide (TMPFPIP), a reversible inhibitor of the gastric H+/K+-ATPase, was retained in its predefined conformation and was allowed full torsional flexibility in docking, the ligands localized to discrete binding volumes in the E1 model and to a single central binding space, together with secondary peripheral locations, in the E2 conformation. The results of these binding studies are in good agreement with current site-directed mutagenesis data and support the suggestion that the binding site is proximal to the loop between TM5 and TM6 and TM8, the transmembrane (TM) region considered important for cation translocation. Furthermore, the results of the simulation with the flexible ligand complement the solid-state NMR structural constraints of this inhibitor when bound in situ to the protein. |
| Starting Page | 30 |
| Ending Page | 49 |
| Page Count | 20 |
| File Format | PDF HTM / HTML |
| Alternate Webpage(s) | http://www.bioch.ox.ac.uk/oubsu/pdfs/KimJMC.pdf |
| PubMed reference number | 16279772v1 |
| Volume Number | 48 |
| Issue Number | 23 |
| Journal | Journal of medicinal chemistry |
| Language | English |
| Access Restriction | Open |
| Subject Keyword | Binding Sites Calcium ion Cations Complement System Proteins Docking -molecular interaction Entity Name Part Qualifier - adopted Estradiol Homologous Gene Homology Modeling Iodides Ligands Magnetic Resonance Imaging Polyposis, Gastric TPM3 wt Allele |
| Content Type | Text |
| Resource Type | Article |
