2026-11-07_00000103|ligand|36KK

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with spirocyclic inhibitor 14; X-ray diffraction 2.10Å
Protein #1 1081 residues (33% resolved)

MDAVPDTKGSSGPPRGTPETKNNKKNLQEARRKGRMDRSKAEEEMSNELQNLDVQGKSKATGTGLVYVDAFTRFHCLWDASHPECPARVSTVMEMLETEGLLGRCVQVEARAVTEDELLLVHTKEYVELMKSTQNMTEEELKTLAEKYDSVYLHPGFFSSACLSVGSVLQLVDKVMTSQLRNGFSINRPPGHHAQADKMNGFCMFNNLAIAARYAQKRHRVQRVLIVDWDVHHGQGIQYIFEEDPSVLYFSVHRYEDGSFWPHLKESDSSSVGSGAGQGYNINLPWNKVGMESGDYITAFQQLLLPVAYEFQPQLVLVAAGFDAVIGDPKGGMQVSPECFSILTHMLKGVAQGRLVLALEGGYNLQSTAEGVCASMRSLLGDPCPHLPSSGAPCESALKSISKTISDLYPFWKSLQTFEGGPLSEVSPLPAPVCAEVKVSSPITGLVYDQRMMLHHNMWDSHHPELPQRISRIFSRHEELRLLSRCHRIPARLATEEELALCHSSKHISIIKSSEHMKPRDLNRLGDEYNSIFISNESYTCALLAAGSCFNSAQAILTGQVRNAVAIVRPPGHHAEKDTACGFCFFNTAALTARYAQSITRESLRVLIVDWDVHHGNGTQHIFEEDDSVLYISLHRYEDGAFFPNSEDANYDKVGLGKGRGYNVNIPWNGGKMGDPEYMAAFHHLVMPIAREFAPELVLVSAGFDAARGDPLGGFQVTPEGYAHLTHQLMSLAAGRVLIILEGGYNLTSISESMSMCTSMLLGDSPPSLDHLTPLKTSATVSINNVLRAHAPFWSSLRVNIPESLRLSLPSPKPKGKCTPGGKGKKSPRQSTPSQSPGQATHRPDQSGFDELTADLLSLNLNTSTSSNTSPESVAVGGARRKVKPNTHRVSAGLESESPLKLNPEKAGAGDDTDVKAETPNRSISEPVVTCDSSAVKDQESLVLEAAGGNTVQSVLERVFGAQATDVDTMYVVDPLPWCPHLESVRPVPAGGIDVFQPCEECGGEAENWICLFCYKVLCGRYVNQHMVTHGQESGHPVVLSFADLSVWCYACESYVHNKVLHEAKNAAHLVKFGEGIHPFN

MDAVPDTKGSSGPPRGTPETKNNKKNLQEARRKGRMDRSKAEEEMSNELQNLDVQGKSKATGTGLVYVDAFTRFHCLWDASHPECPARVSTVMEMLETEGLLGRCVQVEARAVTEDELLLVHTKEYVELMKSTQNMTEEELKTLAEKYDSVYLHPGFFSSACLSVGSVLQLVDKVMTSQLRNGFSINRPPGHHAQADKMNGFCMFNNLAIAARYAQKRHRVQRVLIVDWDVHHGQGIQYIFEEDPSVLYFSVHRYEDGSFWPHLKESDSSSVGSGAGQGYNINLPWNKVGMESGDYITAFQQLLLPVAYEFQPQLVLVAAGFDAVIGDPKGGMQVSPECFSILTHMLKGVAQGRLVLALEGGYNLQSTAEGVCASMRSLLGDPCPHLPSSGAPCESALKSISKTISDLYPFWKSLQTFEGGPLSEVSPLPAPVCAEVKVSSPITGLVYDQRMMLHHNMWDSHHPELPQRISRIFSRHEELRLLSRCHRIPARLATEEELALCHSSKHISIIKSSEHMKPRDLNRLGDEYNSIFISNESYTCALLAAGSCFNSAQAILTGQVRNAVAIVRPPGHHAEKDTACGFCFFNTAALTARYAQSITRESLRVLIVDWDVHHGNGTQHIFEEDDSVLYISLHRYEDGAFFPNSEDANYDKVGLGKGRGYNVNIPWNGGKMGDPEYMAAFHHLVMPIAREFAPELVLVSAGFDAARGDPLGGFQVTPEGYAHLTHQLMSLAAGRVLIILEGGYNLTSISESMSMCTSMLLGDSPPSLDHLTPLKTSATVSINNVLRAHAPFWSSLRVNIPESLRLSLPSPKPKGKCTPGGKGKKSPRQSTPSQSPGQATHRPDQSGFDELTADLLSLNLNTSTSSNTSPESVAVGGARRKVKPNTHRVSAGLESESPLKLNPEKAGAGDDTDVKAETPNRSISEPVVTCDSSAVKDQESLVLEAAGGNTVQSVLERVFGAQATDVDTMYVVDPLPWCPHLESVRPVPAGGIDVFQPCEECGGEAENWICLFCYKVLCGRYVNQHMVTHGQESGHPVVLSFADLSVWCYACESYVHNKVLHEAKNAAHLVKFGEGIHPFN
Non polymer #2 A1DKB

InChI=1S/C27H28FN5O3/c28-24-15-21(25(34)30-36)8-9-22(24)18-32-19-33(23-6-2-1-3-7-23)27(26(32)35)10-13-31(14-11-27)17-20-5-4-12-29-16-20/h1-9,12,15-16,36H,10-11,13-14,17-19H2,(H,30,34)

c1ccc(cc1)N2CN(C(=O)C23CCN(CC3)Cc4cccnc4)Cc5ccc(cc5F)C(=O)NO
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