7JOM

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with TO-317

Summary for 7JOM

• Entry DOI: 10.2210/pdb7jom/pdb
• Descriptor: Hdac6 protein, N-hydroxy-4-({[(pyridin-3-yl)methyl][(2,3,4,5-tetrafluorophenyl)sulfonyl]amino}methyl)benzamide, 1,2-ETHANEDIOL, ... (7 entities in total)
• Functional Keywords: hydrolase, histone deacetylase, inhibitor, metallohydrolase, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Danio rerio (Zebrafish)
• Total number of polymer chains: 2
• Total formula weight: 82206.40

Authors

Watson, P.R.,Christianson, D.W. (deposition date: 2020-08-06, release date: 2021-06-16, Last modification date: 2023-10-18)

Primary citation

Olaoye, O.O.,Watson, P.R.,Nawar, N.,Geletu, M.,Sedighi, A.,Bukhari, S.,Raouf, Y.S.,Manaswiyoungkul, P.,Erdogan, F.,Abdeldayem, A.,Cabral, A.D.,Hassan, M.M.,Toutah, K.,Shouksmith, A.E.,Gawel, J.M.,Israelian, J.,Radu, T.B.,Kachhiyapatel, N.,de Araujo, E.D.,Christianson, D.W.,Gunning, P.T.
Unique Molecular Interaction with the Histone Deacetylase 6 Catalytic Tunnel: Crystallographic and Biological Characterization of a Model Chemotype.
J.Med.Chem., 64:2691-2704, 2021

PubMed Abstract: Histone deacetylase 6 (HDAC6) is involved in multiple regulatory processes, ranging from cellular stress to intracellular transport. Inhibition of aberrant HDAC6 activity in several cancers and neurological diseases has been shown to be efficacious in both preclinical and clinical studies. While selective HDAC6 targeting has been pursued as an alternative to pan-HDAC drugs, identifying truly selective molecular templates has not been trivial. Herein, we report a structure-activity relationship study yielding , which potently binds HDAC6 catalytic domain 2 ( = 0.7 nM) and inhibits the enzyme function (IC = 2 nM). exhibits 158-fold selectivity for HDAC6 over other HDAC isozymes by binding the catalytic Zn and, uniquely, making a never seen before direct hydrogen bond with the Zn coordinating residue, His614. This novel structural motif targeting the second-sphere His614 interaction, observed in a 1.84 Å resolution crystal structure with HDAC6 from zebrafish, can provide new pharmacophores for identifying enthalpically driven, high-affinity, HDAC6-selective inhibitors.

PubMed: 33576627
DOI: 10.1021/acs.jmedchem.0c01922

Experimental method

X-RAY DIFFRACTION (1.84 Å)