7NXM
Structure of human cathepsin K in complex with the selective activity-based probe Gu3416
Summary for 7NXM
| Entry DOI | 10.2210/pdb7nxm/pdb |
| Descriptor | Cathepsin K, SULFATE ION, N-(4-(dibenzylamino)-4-oxobutyl)-2-(5-(dimethylamino)pentanamido)-4-methylpentanamide, ... (4 entities in total) |
| Functional Keywords | hydrolase, inhibitor, complex, activity-based probe, acrylamide inhibitor |
| Biological source | Homo sapiens (Human) |
| Total number of polymer chains | 1 |
| Total formula weight | 24299.46 |
| Authors | Busa, M.,Benysek, J.,Lemke, C.,Gutschow, M.,Mares, M. (deposition date: 2021-03-18, release date: 2021-09-08, Last modification date: 2024-01-31) |
| Primary citation | Lemke, C.,Benysek, J.,Brajtenbach, D.,Breuer, C.,Jilkova, A.,Horn, M.,Busa, M.,Ulrychova, L.,Illies, A.,Kubatzky, K.F.,Bartz, U.,Mares, M.,Gutschow, M. An Activity-Based Probe for Cathepsin K Imaging with Excellent Potency and Selectivity. J.Med.Chem., 64:13793-13806, 2021 Cited by PubMed Abstract: The cysteine protease cathepsin K is a target for the treatment of diseases associated with high bone turnover. Cathepsin K is mainly expressed in osteoclasts and responsible for the destruction of the proteinaceous components of the bone matrix. We designed various fluorescent activity-based probes (ABPs) and their precursors that bind to and inactivate cathepsin K. ABP exhibited extraordinary potency (/ = 35,300 Ms) and selectivity for human cathepsin K. Crystal structures of cathepsin K in complex with ABP and its nonfluorescent precursor were determined to characterize the binding mode of this new type of acrylamide-based Michael acceptor with the particular orientation of the dibenzylamine moiety to the primed subsite region. The cyanine-5 containing probe allowed for sensitive detection of cathepsin K, selective visualization in complex proteomes, and live cell imaging of a human osteosarcoma cell line, underlining its applicability in a pathophysiological environment. PubMed: 34473502DOI: 10.1021/acs.jmedchem.1c01178 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.72 Å) |
Structure validation
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