2026-11-07_00000104|ligand|36KL

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with spirocyclic inhibitor 20a; X-ray diffraction 2.03Å
Protein #1 1081 residues (32% resolved)

MDAVPDTKGSSGPPRGTPETKNNKKNLQEARRKGRMDRSKAEEEMSNELQNLDVQGKSKATGTGLVYVDAFTRFHCLWDASHPECPARVSTVMEMLETEGLLGRCVQVEARAVTEDELLLVHTKEYVELMKSTQNMTEEELKTLAEKYDSVYLHPGFFSSACLSVGSVLQLVDKVMTSQLRNGFSINRPPGHHAQADKMNGFCMFNNLAIAARYAQKRHRVQRVLIVDWDVHHGQGIQYIFEEDPSVLYFSVHRYEDGSFWPHLKESDSSSVGSGAGQGYNINLPWNKVGMESGDYITAFQQLLLPVAYEFQPQLVLVAAGFDAVIGDPKGGMQVSPECFSILTHMLKGVAQGRLVLALEGGYNLQSTAEGVCASMRSLLGDPCPHLPSSGAPCESALKSISKTISDLYPFWKSLQTFEGGPLSEVSPLPAPVCAEVKVSSPITGLVYDQRMMLHHNMWDSHHPELPQRISRIFSRHEELRLLSRCHRIPARLATEEELALCHSSKHISIIKSSEHMKPRDLNRLGDEYNSIFISNESYTCALLAAGSCFNSAQAILTGQVRNAVAIVRPPGHHAEKDTACGFCFFNTAALTARYAQSITRESLRVLIVDWDVHHGNGTQHIFEEDDSVLYISLHRYEDGAFFPNSEDANYDKVGLGKGRGYNVNIPWNGGKMGDPEYMAAFHHLVMPIAREFAPELVLVSAGFDAARGDPLGGFQVTPEGYAHLTHQLMSLAAGRVLIILEGGYNLTSISESMSMCTSMLLGDSPPSLDHLTPLKTSATVSINNVLRAHAPFWSSLRVNIPESLRLSLPSPKPKGKCTPGGKGKKSPRQSTPSQSPGQATHRPDQSGFDELTADLLSLNLNTSTSSNTSPESVAVGGARRKVKPNTHRVSAGLESESPLKLNPEKAGAGDDTDVKAETPNRSISEPVVTCDSSAVKDQESLVLEAAGGNTVQSVLERVFGAQATDVDTMYVVDPLPWCPHLESVRPVPAGGIDVFQPCEECGGEAENWICLFCYKVLCGRYVNQHMVTHGQESGHPVVLSFADLSVWCYACESYVHNKVLHEAKNAAHLVKFGEGIHPFN

MDAVPDTKGSSGPPRGTPETKNNKKNLQEARRKGRMDRSKAEEEMSNELQNLDVQGKSKATGTGLVYVDAFTRFHCLWDASHPECPARVSTVMEMLETEGLLGRCVQVEARAVTEDELLLVHTKEYVELMKSTQNMTEEELKTLAEKYDSVYLHPGFFSSACLSVGSVLQLVDKVMTSQLRNGFSINRPPGHHAQADKMNGFCMFNNLAIAARYAQKRHRVQRVLIVDWDVHHGQGIQYIFEEDPSVLYFSVHRYEDGSFWPHLKESDSSSVGSGAGQGYNINLPWNKVGMESGDYITAFQQLLLPVAYEFQPQLVLVAAGFDAVIGDPKGGMQVSPECFSILTHMLKGVAQGRLVLALEGGYNLQSTAEGVCASMRSLLGDPCPHLPSSGAPCESALKSISKTISDLYPFWKSLQTFEGGPLSEVSPLPAPVCAEVKVSSPITGLVYDQRMMLHHNMWDSHHPELPQRISRIFSRHEELRLLSRCHRIPARLATEEELALCHSSKHISIIKSSEHMKPRDLNRLGDEYNSIFISNESYTCALLAAGSCFNSAQAILTGQVRNAVAIVRPPGHHAEKDTACGFCFFNTAALTARYAQSITRESLRVLIVDWDVHHGNGTQHIFEEDDSVLYISLHRYEDGAFFPNSEDANYDKVGLGKGRGYNVNIPWNGGKMGDPEYMAAFHHLVMPIAREFAPELVLVSAGFDAARGDPLGGFQVTPEGYAHLTHQLMSLAAGRVLIILEGGYNLTSISESMSMCTSMLLGDSPPSLDHLTPLKTSATVSINNVLRAHAPFWSSLRVNIPESLRLSLPSPKPKGKCTPGGKGKKSPRQSTPSQSPGQATHRPDQSGFDELTADLLSLNLNTSTSSNTSPESVAVGGARRKVKPNTHRVSAGLESESPLKLNPEKAGAGDDTDVKAETPNRSISEPVVTCDSSAVKDQESLVLEAAGGNTVQSVLERVFGAQATDVDTMYVVDPLPWCPHLESVRPVPAGGIDVFQPCEECGGEAENWICLFCYKVLCGRYVNQHMVTHGQESGHPVVLSFADLSVWCYACESYVHNKVLHEAKNAAHLVKFGEGIHPFN
Non polymer #2 A1DKA

InChI=1S/C36H45N5O6/c1-35(2,3)47-34(45)37-30(22-26-10-6-4-7-11-26)31(42)24-39-20-18-36(19-21-39)33(44)40(25-41(36)29-12-8-5-9-13-29)23-27-14-16-28(17-15-27)32(43)38-46/h4-17,30-31,42,46H,18-25H2,1-3H3,(H,37,45)(H,38,43)/t30-,31+/m0/s1

CC(C)(C)OC(=O)N[C@@H](Cc1ccccc1)[C@@H](CN2CCC3(CC2)C(=O)N(CN3c4ccccc4)Cc5ccc(cc5)C(=O)NO)O
Non polymer #3 EDO

InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2

C(CO)O
Non polymer #4 K

InChI=1S/K/q+1

[K+]
Non polymer #5 ZN

InChI=1S/Zn/q+2

[Zn+2]
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Reference