2026-11-07_00000105|ligand|36KM

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with spirocyclic inhibitor 15; X-ray diffraction 2.07Å
Protein #1 1081 residues (33% resolved)

MDAVPDTKGSSGPPRGTPETKNNKKNLQEARRKGRMDRSKAEEEMSNELQNLDVQGKSKATGTGLVYVDAFTRFHCLWDASHPECPARVSTVMEMLETEGLLGRCVQVEARAVTEDELLLVHTKEYVELMKSTQNMTEEELKTLAEKYDSVYLHPGFFSSACLSVGSVLQLVDKVMTSQLRNGFSINRPPGHHAQADKMNGFCMFNNLAIAARYAQKRHRVQRVLIVDWDVHHGQGIQYIFEEDPSVLYFSVHRYEDGSFWPHLKESDSSSVGSGAGQGYNINLPWNKVGMESGDYITAFQQLLLPVAYEFQPQLVLVAAGFDAVIGDPKGGMQVSPECFSILTHMLKGVAQGRLVLALEGGYNLQSTAEGVCASMRSLLGDPCPHLPSSGAPCESALKSISKTISDLYPFWKSLQTFEGGPLSEVSPLPAPVCAEVKVSSPITGLVYDQRMMLHHNMWDSHHPELPQRISRIFSRHEELRLLSRCHRIPARLATEEELALCHSSKHISIIKSSEHMKPRDLNRLGDEYNSIFISNESYTCALLAAGSCFNSAQAILTGQVRNAVAIVRPPGHHAEKDTACGFCFFNTAALTARYAQSITRESLRVLIVDWDVHHGNGTQHIFEEDDSVLYISLHRYEDGAFFPNSEDANYDKVGLGKGRGYNVNIPWNGGKMGDPEYMAAFHHLVMPIAREFAPELVLVSAGFDAARGDPLGGFQVTPEGYAHLTHQLMSLAAGRVLIILEGGYNLTSISESMSMCTSMLLGDSPPSLDHLTPLKTSATVSINNVLRAHAPFWSSLRVNIPESLRLSLPSPKPKGKCTPGGKGKKSPRQSTPSQSPGQATHRPDQSGFDELTADLLSLNLNTSTSSNTSPESVAVGGARRKVKPNTHRVSAGLESESPLKLNPEKAGAGDDTDVKAETPNRSISEPVVTCDSSAVKDQESLVLEAAGGNTVQSVLERVFGAQATDVDTMYVVDPLPWCPHLESVRPVPAGGIDVFQPCEECGGEAENWICLFCYKVLCGRYVNQHMVTHGQESGHPVVLSFADLSVWCYACESYVHNKVLHEAKNAAHLVKFGEGIHPFN

MDAVPDTKGSSGPPRGTPETKNNKKNLQEARRKGRMDRSKAEEEMSNELQNLDVQGKSKATGTGLVYVDAFTRFHCLWDASHPECPARVSTVMEMLETEGLLGRCVQVEARAVTEDELLLVHTKEYVELMKSTQNMTEEELKTLAEKYDSVYLHPGFFSSACLSVGSVLQLVDKVMTSQLRNGFSINRPPGHHAQADKMNGFCMFNNLAIAARYAQKRHRVQRVLIVDWDVHHGQGIQYIFEEDPSVLYFSVHRYEDGSFWPHLKESDSSSVGSGAGQGYNINLPWNKVGMESGDYITAFQQLLLPVAYEFQPQLVLVAAGFDAVIGDPKGGMQVSPECFSILTHMLKGVAQGRLVLALEGGYNLQSTAEGVCASMRSLLGDPCPHLPSSGAPCESALKSISKTISDLYPFWKSLQTFEGGPLSEVSPLPAPVCAEVKVSSPITGLVYDQRMMLHHNMWDSHHPELPQRISRIFSRHEELRLLSRCHRIPARLATEEELALCHSSKHISIIKSSEHMKPRDLNRLGDEYNSIFISNESYTCALLAAGSCFNSAQAILTGQVRNAVAIVRPPGHHAEKDTACGFCFFNTAALTARYAQSITRESLRVLIVDWDVHHGNGTQHIFEEDDSVLYISLHRYEDGAFFPNSEDANYDKVGLGKGRGYNVNIPWNGGKMGDPEYMAAFHHLVMPIAREFAPELVLVSAGFDAARGDPLGGFQVTPEGYAHLTHQLMSLAAGRVLIILEGGYNLTSISESMSMCTSMLLGDSPPSLDHLTPLKTSATVSINNVLRAHAPFWSSLRVNIPESLRLSLPSPKPKGKCTPGGKGKKSPRQSTPSQSPGQATHRPDQSGFDELTADLLSLNLNTSTSSNTSPESVAVGGARRKVKPNTHRVSAGLESESPLKLNPEKAGAGDDTDVKAETPNRSISEPVVTCDSSAVKDQESLVLEAAGGNTVQSVLERVFGAQATDVDTMYVVDPLPWCPHLESVRPVPAGGIDVFQPCEECGGEAENWICLFCYKVLCGRYVNQHMVTHGQESGHPVVLSFADLSVWCYACESYVHNKVLHEAKNAAHLVKFGEGIHPFN
Non polymer #2 A1DJ1

InChI=1S/C22H24F2N4O3/c1-26-9-7-22(8-10-26)21(30)27(14-28(22)16-5-3-2-4-6-16)13-17-18(23)11-15(12-19(17)24)20(29)25-31/h2-6,11-12,31H,7-10,13-14H2,1H3,(H,25,29)

CN1CCC2(CC1)C(=O)N(CN2c3ccccc3)Cc4c(cc(cc4F)C(=O)NO)F
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