2026-11-07_00000102|ligand|36KJ

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with spirocyclic inhibitor 20b; X-ray diffraction 1.86Å
Protein #1 1081 residues (32% resolved)

MDAVPDTKGSSGPPRGTPETKNNKKNLQEARRKGRMDRSKAEEEMSNELQNLDVQGKSKATGTGLVYVDAFTRFHCLWDASHPECPARVSTVMEMLETEGLLGRCVQVEARAVTEDELLLVHTKEYVELMKSTQNMTEEELKTLAEKYDSVYLHPGFFSSACLSVGSVLQLVDKVMTSQLRNGFSINRPPGHHAQADKMNGFCMFNNLAIAARYAQKRHRVQRVLIVDWDVHHGQGIQYIFEEDPSVLYFSVHRYEDGSFWPHLKESDSSSVGSGAGQGYNINLPWNKVGMESGDYITAFQQLLLPVAYEFQPQLVLVAAGFDAVIGDPKGGMQVSPECFSILTHMLKGVAQGRLVLALEGGYNLQSTAEGVCASMRSLLGDPCPHLPSSGAPCESALKSISKTISDLYPFWKSLQTFEGGPLSEVSPLPAPVCAEVKVSSPITGLVYDQRMMLHHNMWDSHHPELPQRISRIFSRHEELRLLSRCHRIPARLATEEELALCHSSKHISIIKSSEHMKPRDLNRLGDEYNSIFISNESYTCALLAAGSCFNSAQAILTGQVRNAVAIVRPPGHHAEKDTACGFCFFNTAALTARYAQSITRESLRVLIVDWDVHHGNGTQHIFEEDDSVLYISLHRYEDGAFFPNSEDANYDKVGLGKGRGYNVNIPWNGGKMGDPEYMAAFHHLVMPIAREFAPELVLVSAGFDAARGDPLGGFQVTPEGYAHLTHQLMSLAAGRVLIILEGGYNLTSISESMSMCTSMLLGDSPPSLDHLTPLKTSATVSINNVLRAHAPFWSSLRVNIPESLRLSLPSPKPKGKCTPGGKGKKSPRQSTPSQSPGQATHRPDQSGFDELTADLLSLNLNTSTSSNTSPESVAVGGARRKVKPNTHRVSAGLESESPLKLNPEKAGAGDDTDVKAETPNRSISEPVVTCDSSAVKDQESLVLEAAGGNTVQSVLERVFGAQATDVDTMYVVDPLPWCPHLESVRPVPAGGIDVFQPCEECGGEAENWICLFCYKVLCGRYVNQHMVTHGQESGHPVVLSFADLSVWCYACESYVHNKVLHEAKNAAHLVKFGEGIHPFN

MDAVPDTKGSSGPPRGTPETKNNKKNLQEARRKGRMDRSKAEEEMSNELQNLDVQGKSKATGTGLVYVDAFTRFHCLWDASHPECPARVSTVMEMLETEGLLGRCVQVEARAVTEDELLLVHTKEYVELMKSTQNMTEEELKTLAEKYDSVYLHPGFFSSACLSVGSVLQLVDKVMTSQLRNGFSINRPPGHHAQADKMNGFCMFNNLAIAARYAQKRHRVQRVLIVDWDVHHGQGIQYIFEEDPSVLYFSVHRYEDGSFWPHLKESDSSSVGSGAGQGYNINLPWNKVGMESGDYITAFQQLLLPVAYEFQPQLVLVAAGFDAVIGDPKGGMQVSPECFSILTHMLKGVAQGRLVLALEGGYNLQSTAEGVCASMRSLLGDPCPHLPSSGAPCESALKSISKTISDLYPFWKSLQTFEGGPLSEVSPLPAPVCAEVKVSSPITGLVYDQRMMLHHNMWDSHHPELPQRISRIFSRHEELRLLSRCHRIPARLATEEELALCHSSKHISIIKSSEHMKPRDLNRLGDEYNSIFISNESYTCALLAAGSCFNSAQAILTGQVRNAVAIVRPPGHHAEKDTACGFCFFNTAALTARYAQSITRESLRVLIVDWDVHHGNGTQHIFEEDDSVLYISLHRYEDGAFFPNSEDANYDKVGLGKGRGYNVNIPWNGGKMGDPEYMAAFHHLVMPIAREFAPELVLVSAGFDAARGDPLGGFQVTPEGYAHLTHQLMSLAAGRVLIILEGGYNLTSISESMSMCTSMLLGDSPPSLDHLTPLKTSATVSINNVLRAHAPFWSSLRVNIPESLRLSLPSPKPKGKCTPGGKGKKSPRQSTPSQSPGQATHRPDQSGFDELTADLLSLNLNTSTSSNTSPESVAVGGARRKVKPNTHRVSAGLESESPLKLNPEKAGAGDDTDVKAETPNRSISEPVVTCDSSAVKDQESLVLEAAGGNTVQSVLERVFGAQATDVDTMYVVDPLPWCPHLESVRPVPAGGIDVFQPCEECGGEAENWICLFCYKVLCGRYVNQHMVTHGQESGHPVVLSFADLSVWCYACESYVHNKVLHEAKNAAHLVKFGEGIHPFN
Non polymer #2 A1DJZ

InChI=1S/C36H44FN5O6/c1-35(2,3)48-34(46)38-30(20-25-10-6-4-7-11-25)31(43)23-40-18-16-36(17-19-40)33(45)41(24-42(36)28-12-8-5-9-13-28)22-27-15-14-26(21-29(27)37)32(44)39-47/h4-15,21,30-31,43,47H,16-20,22-24H2,1-3H3,(H,38,46)(H,39,44)/t30-,31+/m0/s1

CC(C)(C)OC(=O)N[C@@H](Cc1ccccc1)[C@@H](CN2CCC3(CC2)C(=O)N(CN3c4ccccc4)Cc5ccc(cc5F)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