7U8Z
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) complexed with fluorinated peptoid inhibitor
Summary for 7U8Z
| Entry DOI | 10.2210/pdb7u8z/pdb |
| Descriptor | Hdac6 protein, ACETATE ION, 4-({N-[2-(benzylamino)-2-oxoethyl]-4-(dimethylamino)benzamido}methyl)-3-fluoro-N-hydroxybenzamide, ... (9 entities in total) |
| Functional Keywords | hydrolase, histone deacetylase, inhibitor, metallohydrolase, hydrolase-inhibitor complex, hydrolase/inhibitor |
| Biological source | Danio rerio (zebrafish) |
| Total number of polymer chains | 4 |
| Total formula weight | 164256.01 |
| Authors | Watson, P.R.,Cragin, A.D.,Christianson, D.W. (deposition date: 2022-03-09, release date: 2022-11-23, Last modification date: 2023-10-25) |
| Primary citation | Ressing, N.,Schliehe-Diecks, J.,Watson, P.R.,Sonnichsen, M.,Cragin, A.D.,Scholer, A.,Yang, J.,Schaker-Hubner, L.,Borkhardt, A.,Christianson, D.W.,Bhatia, S.,Hansen, F.K. Development of Fluorinated Peptoid-Based Histone Deacetylase (HDAC) Inhibitors for Therapy-Resistant Acute Leukemia. J.Med.Chem., 65:15457-15472, 2022 Cited by PubMed Abstract: Using a microwave-assisted protocol, we synthesized 16 peptoid-capped HDAC inhibitors (HDACi) with fluorinated linkers and identified two hit compounds. In biochemical and cellular assays, stood out as a potent unselective HDACi with remarkable cytotoxic potential against different therapy-resistant leukemia cell lines. demonstrated prominent antileukemic activity with low cytotoxic activity toward healthy cells. Moreover, exhibited synergistic interactions with the DNA methyltransferase inhibitor decitabine in AML cell lines. The comparison of crystal structures of HDAC6 complexes with and its nonfluorinated counterpart revealed a similar occupation of the L1 loop pocket but slight differences in zinc coordination. The substitution pattern of the acyl residue turned out to be crucial in terms of isoform selectivity. The introduction of an isopropyl group onto the phenyl ring provided the highly HDAC6-selective inhibitor , which demonstrated moderate synergy with decitabine and exceeded the HDAC6 selectivity of tubastatin A. PubMed: 36351184DOI: 10.1021/acs.jmedchem.2c01418 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.85 Å) |
Structure validation
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