5NYH
Crystal Structure of Hsp90-alpha N-Domain in complex with Indazole derivative
Summary for 5NYH
| Entry DOI | 10.2210/pdb5nyh/pdb |
| Related | 5NYD |
| Descriptor | Heat shock protein HSP 90-alpha, ~{N}-methyl-~{N}-(4-morpholin-4-ylphenyl)-6-oxidanyl-3-pyrrolidin-1-ylcarbonyl-2~{H}-indazole-5-carboxamide (3 entities in total) |
| Functional Keywords | chaperone |
| Biological source | Homo sapiens (Human) |
| Total number of polymer chains | 1 |
| Total formula weight | 26163.32 |
| Authors | Amaral, M. (deposition date: 2017-05-11, release date: 2018-04-18, Last modification date: 2024-05-08) |
| Primary citation | Schuetz, D.A.,Richter, L.,Amaral, M.,Grandits, M.,Gradler, U.,Musil, D.,Buchstaller, H.P.,Eggenweiler, H.M.,Frech, M.,Ecker, G.F. Ligand Desolvation Steers On-Rate and Impacts Drug Residence Time of Heat Shock Protein 90 (Hsp90) Inhibitors. J. Med. Chem., 61:4397-4411, 2018 Cited by PubMed Abstract: Residence time and more recently the association rate constant k are increasingly acknowledged as important parameters for in vivo efficacy and safety of drugs. However, their broader consideration in drug development is limited by a lack of knowledge of how to optimize these parameters. In this study on a set of 176 heat shock protein 90 inhibitors, structure-kinetic relationships, X-ray crystallography, and molecular dynamics simulations were combined to retrieve a concrete scheme of how to rationally slow down on-rates. We discovered that an increased ligand desolvation barrier by introducing polar substituents resulted in a significant k decrease. The slowdown was accomplished by introducing polar moieties to those parts of the ligand that point toward a hydrophobic cavity. We validated this scheme by increasing polarity of three Hsp90 inhibitors and observed a 9-, 13-, and 45-fold slowdown of on-rates and a 9-fold prolongation in residence time. This prolongation was driven by transition state destabilization rather than ground state stabilization. PubMed: 29701469DOI: 10.1021/acs.jmedchem.8b00080 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.65 Å) |
Structure validation
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