2026-11-07_00000100|ligand|36KH

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with spirocyclic inhibitor 13; X-ray diffraction 2.28Å
Protein #1 1081 residues (33% resolved)

MDAVPDTKGSSGPPRGTPETKNNKKNLQEARRKGRMDRSKAEEEMSNELQNLDVQGKSKATGTGLVYVDAFTRFHCLWDASHPECPARVSTVMEMLETEGLLGRCVQVEARAVTEDELLLVHTKEYVELMKSTQNMTEEELKTLAEKYDSVYLHPGFFSSACLSVGSVLQLVDKVMTSQLRNGFSINRPPGHHAQADKMNGFCMFNNLAIAARYAQKRHRVQRVLIVDWDVHHGQGIQYIFEEDPSVLYFSVHRYEDGSFWPHLKESDSSSVGSGAGQGYNINLPWNKVGMESGDYITAFQQLLLPVAYEFQPQLVLVAAGFDAVIGDPKGGMQVSPECFSILTHMLKGVAQGRLVLALEGGYNLQSTAEGVCASMRSLLGDPCPHLPSSGAPCESALKSISKTISDLYPFWKSLQTFEGGPLSEVSPLPAPVCAEVKVSSPITGLVYDQRMMLHHNMWDSHHPELPQRISRIFSRHEELRLLSRCHRIPARLATEEELALCHSSKHISIIKSSEHMKPRDLNRLGDEYNSIFISNESYTCALLAAGSCFNSAQAILTGQVRNAVAIVRPPGHHAEKDTACGFCFFNTAALTARYAQSITRESLRVLIVDWDVHHGNGTQHIFEEDDSVLYISLHRYEDGAFFPNSEDANYDKVGLGKGRGYNVNIPWNGGKMGDPEYMAAFHHLVMPIAREFAPELVLVSAGFDAARGDPLGGFQVTPEGYAHLTHQLMSLAAGRVLIILEGGYNLTSISESMSMCTSMLLGDSPPSLDHLTPLKTSATVSINNVLRAHAPFWSSLRVNIPESLRLSLPSPKPKGKCTPGGKGKKSPRQSTPSQSPGQATHRPDQSGFDELTADLLSLNLNTSTSSNTSPESVAVGGARRKVKPNTHRVSAGLESESPLKLNPEKAGAGDDTDVKAETPNRSISEPVVTCDSSAVKDQESLVLEAAGGNTVQSVLERVFGAQATDVDTMYVVDPLPWCPHLESVRPVPAGGIDVFQPCEECGGEAENWICLFCYKVLCGRYVNQHMVTHGQESGHPVVLSFADLSVWCYACESYVHNKVLHEAKNAAHLVKFGEGIHPFN

MDAVPDTKGSSGPPRGTPETKNNKKNLQEARRKGRMDRSKAEEEMSNELQNLDVQGKSKATGTGLVYVDAFTRFHCLWDASHPECPARVSTVMEMLETEGLLGRCVQVEARAVTEDELLLVHTKEYVELMKSTQNMTEEELKTLAEKYDSVYLHPGFFSSACLSVGSVLQLVDKVMTSQLRNGFSINRPPGHHAQADKMNGFCMFNNLAIAARYAQKRHRVQRVLIVDWDVHHGQGIQYIFEEDPSVLYFSVHRYEDGSFWPHLKESDSSSVGSGAGQGYNINLPWNKVGMESGDYITAFQQLLLPVAYEFQPQLVLVAAGFDAVIGDPKGGMQVSPECFSILTHMLKGVAQGRLVLALEGGYNLQSTAEGVCASMRSLLGDPCPHLPSSGAPCESALKSISKTISDLYPFWKSLQTFEGGPLSEVSPLPAPVCAEVKVSSPITGLVYDQRMMLHHNMWDSHHPELPQRISRIFSRHEELRLLSRCHRIPARLATEEELALCHSSKHISIIKSSEHMKPRDLNRLGDEYNSIFISNESYTCALLAAGSCFNSAQAILTGQVRNAVAIVRPPGHHAEKDTACGFCFFNTAALTARYAQSITRESLRVLIVDWDVHHGNGTQHIFEEDDSVLYISLHRYEDGAFFPNSEDANYDKVGLGKGRGYNVNIPWNGGKMGDPEYMAAFHHLVMPIAREFAPELVLVSAGFDAARGDPLGGFQVTPEGYAHLTHQLMSLAAGRVLIILEGGYNLTSISESMSMCTSMLLGDSPPSLDHLTPLKTSATVSINNVLRAHAPFWSSLRVNIPESLRLSLPSPKPKGKCTPGGKGKKSPRQSTPSQSPGQATHRPDQSGFDELTADLLSLNLNTSTSSNTSPESVAVGGARRKVKPNTHRVSAGLESESPLKLNPEKAGAGDDTDVKAETPNRSISEPVVTCDSSAVKDQESLVLEAAGGNTVQSVLERVFGAQATDVDTMYVVDPLPWCPHLESVRPVPAGGIDVFQPCEECGGEAENWICLFCYKVLCGRYVNQHMVTHGQESGHPVVLSFADLSVWCYACESYVHNKVLHEAKNAAHLVKFGEGIHPFN
Non polymer #2 A1DJ0

InChI=1S/C22H25FN4O3/c1-25-11-9-22(10-12-25)21(29)26(15-27(22)18-5-3-2-4-6-18)14-17-8-7-16(13-19(17)23)20(28)24-30/h2-8,13,30H,9-12,14-15H2,1H3,(H,24,28)

CN1CCC2(CC1)C(=O)N(CN2c3ccccc3)Cc4ccc(cc4F)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]
Download coordinates
Download coordinates
Reference