9DM6
Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with an ethylhydrazide inhibitor
This is a non-PDB format compatible entry.
Summary for 9DM6
| Entry DOI | 10.2210/pdb9dm6/pdb |
| Descriptor | Hdac6 protein, N-[2-(benzylamino)-2-oxoethyl]-4-(dimethylamino)-N-{[4-(2-ethylhydrazine-1-carbonyl)phenyl]methyl}benzamide, 1,2-ETHANEDIOL, ... (6 entities in total) |
| Functional Keywords | hydrolase, histone deacetylase, inhibitor, metallohydrolase |
| Biological source | Danio rerio (zebrafish) |
| Total number of polymer chains | 4 |
| Total formula weight | 164473.61 |
| Authors | Gaynes, M.N.,Watson, P.R.,Konig, B.,Christianson, D.W. (deposition date: 2024-09-12, release date: 2025-02-26, Last modification date: 2025-03-12) |
| Primary citation | Stopper, D.,Biermann, L.,Watson, P.R.,Li, J.,Konig, B.,Gaynes, M.N.,Pessanha de Carvalho, L.,Klose, J.,Hanl, M.,Hamacher, A.,Schaker-Hubner, L.,Ramsbeck, D.,Held, J.,Christianson, D.W.,Kassack, M.U.,Hansen, F.K. Exploring Alternative Zinc-Binding Groups in Histone Deacetylase (HDAC) Inhibitors Uncovers DS-103 as a Potent Ethylhydrazide-Based HDAC Inhibitor with Chemosensitizing Properties. J.Med.Chem., 68:4426-4452, 2025 Cited by PubMed Abstract: In this work, we synthesized a series of peptoid-based histone deacetylase (HDAC) inhibitors with variations in the linker region and zinc-binding groups. All compounds were investigated for their HDAC inhibition, antiplasmodial activity, and cytotoxicity against native and cisplatin-resistant carcinoma cell lines. The ethylhydrazide () proved to be the most effective compound in these primary screenings. showed nanomolar inhibition of class I HDACs and of HDAC6 (class IIb). To further investigate the binding mode of , a crystal structure of in complex with HDAC6 was obtained, which represents the first reported crystal structure of an alkylhydrazide in complex with an HDAC enzyme. Importantly, completely reversed cisplatin resistance in two different platinum-resistant solid cancer cell lines and demonstrated strong synergism with cisplatin. The synergistic anticancer effects are mediated by increased DNA damage and p21 expression, resulting in caspase-mediated apoptosis and cell death. PubMed: 39946728DOI: 10.1021/acs.jmedchem.4c02373 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.4 Å) |
Structure validation
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