Histone deacetylase 3D structures

3D Structures of histone deacetylase

Updated on 29-March-2026

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• HDAC class I
• HDAC1
  • 4bkx – hHDAC1 + MTA1 – human
    
  • 3hgq, 3hgt – hHDAC1 subunit 3
    
  • 5icn – hHDAC1 + MTA1 + peptide
    
  • 7ao8, 7ao9 – hHDAC1 + MTA1 + MBD2 – Cryo EM
    
  • 7aoa – hHDAC1 + MTA1 + MBD2 + RBBP4 – Cryo EM
    
  • 6z2j, 6z2k – hHDAC1 + DNTTIP1 + Midac deacetylase – Cryo EM
    
  • 8voj, 8vpq, 8vrt – hHDAC1 + CoRest + Lsd1 – Cryo EM
    
  • 5j8j – yHDAC1 residues 457-698 – yeast
    
  • 6z6f, 6z6h, 6z6o, 6z6p – yHDAC1 – Cryo EM
    
• HDAC2
  • 3max – hHDAC2 + amide derivative
    
  • 4lxz, 6g3o – hHDAC2 core domain + SAHA
    
  • 8bpa, 8bpb, 8c60 – hHDAC2 + SIN3B + PF1 – Cryo EM
    
  • 8bpc – hHDAC2 + SIN3B + PF1 + SAHA – Cryo EM
    
  • 8bpa, 8bpb, 8c60 – hHDAC2 + SIN3B + PF1 – Cryo EM
    
  • 8bpc – hHDAC2 + SIN3B + PF1 + SAHA – Cryo EM
    
  • 4ly1, 5iwg, 5ix0, 6wbw, 6wbz, 6xdm, 6xeb, 6xec, 7js8, 7kbh, 7kbg, 7ltg, 7ltk, 7ltl, 7mot, 7mox, 7moy, 7zzo, 7zzp, 7zzr, 7zzs, 7zzt, 7zzv, 7zzw, 8a0b – hHDAC2 core domain + inhibitor
    
  • 6whn, 6who, 6whq, 6whz, 6wi3, 7mos, 7moz – hHDAC2 core domain + peptide macrocycle
    
  • 9dtq – hHDAC2 + CoRest + Lsd1 – Cryo EM
    
  • 9ggm – hHDAC2 + KBTBD4 – Cryo EM
    
  • 9ggl, 9ggn, 9i2c – hHDAC2 + KBTBD4 + molecular glue – Cryo EM
    
  • 7vrr – AtHDAC2a residues 1-95 – Arabidopsis thaliana
    
  • 7vmf, 7vmh – AtHDAC2d residues 1-95
    
  • 7vmi – AtHDAC2c residues 1-95
    
• HDAC3
  • 4a69 – hHDAC3 + nuclear receptor corepressor 2 + inositol tetraphosphate
• HDAC8
  • 3ew8, 3ezp, 3ezt, 3f06 – hHDAC8 (mutant)
    
  • 3sff, 3sfh – hHDAC8 + inhibitor
    
  • 4qa1, 4qa2, 4qa3, 4qa4 - hHDAC8 (mutant) + inhibitor
    
  • 1t64, 3f0r, 5ths – hHDAC8 + trichostatin A
    
  • 5d1b, 5dc5, 5tht, 5thu, 5thv, 7jvw - hHDAC8 (mutant) + amide derivative
    
  • 1t67, 1vkg, 1w22, 3f07, 6oda, 6odb, 6odc - hHDAC8 + amide derivative
    
  • 1t69 - hHDAC8 + SAHA
    
  • 4qa0, 7jvu - hHDAC8 (mutant) + SAHA
    
  • 5fcw, 5fue - hHDAC8 + hydroxamate
    
  • 5vi6 - hHDAC8 + trapoxin A
    
  • 2v5w – hHDAC8 + tripeptide substrate
    
  • 3ewf, 4qa5, 4qa6, 4qa7, 5d1c, 5d1d, 5dc6, 5dc7, 5dc8, 7jvv, 7p3s - hHDAC8 (mutant) + tetrapeptide substrate
    
  • 3rqd - hHDAC8 + largazole
    
  • 4rn0, 4rn1, 4rn2 - hHDAC8 (mutant) + largazole analog
    
  • 5bwz - hHDAC8 (mutant) + droxinostat
    
  • 3mz3 - hHDAC8 (Co) + amide derivative
    
  • 3mz7 - hHDAC8 (Co) (mutant) + amide derivative
    
  • 3mz4 - hHDAC8 (Mn) (mutant) + amide derivative
    
  • 3mz6 - hHDAC8 (Fe) (mutant) + amide derivative
    
  • 2v5x - hHDAC8 (mutant) + octanediamide derivative
    
  • 4bz5 – SmHDAC8 – Schistosoma mansoni
    
  • 4bz7, 4bz8, 4bz9, 4cqf, 6hqy, 6hrq, 6hsh, 6hsz, 6ht8, 6htg, 6hth, 6hti, 6htt, 6htz, 6hu0, 6hu1, 6hu2, 6hu3, 6tld, 7p2s, 7p2t, 7p2u, 7p2v, 7p3s, 7poz – SmHDAC8 + inhibitor
    
  • 6hsf, 6hsg, 6hsk – SmHDAC8 (mutant) + inhibitor
    
  • 4bz6, 6fu1, 6gx3, 6gxa, 6gxu, 6gxw – SmHDAC8 + SAHA
    derivative
    
• HDAC Rpd3
  • 8kc7, 8w9c – yRpd3 + SIN3 + RCO1 + EAF3 – Cryo EM
    
  • 8hxx – yRpd3 + SIN3 + RCO1 + EAF3 + histone H3 – Cryo EM
    
  • 8hxy, 8hy0, 8ihn, 8iht, 8jho, 8kd2, 8kd3, 8kd4, 8kd5, 8kd6, 8kd7, 8tof, 8w9d, 8w9e, 8w9f – yRpd3 + SIN3 + RCO1 + EAF3 + nucleosome – Cryo EM
    
  • 8hpo – yRpd3 in SIN3/HDAC complex – Cryo EM
    
  • 8ga8 – yRpd3 in Rpd3L complex – Cryo EM
    
• HDAC Clr
  • 5ikk – fyClr3 – fission yeast
    
  • 8ifg – fyClr6 + Prw1 + Pst2 + Eaf3 + Cph1 + Cph2 – Cryo EM
    
  • 8i03 – fyClr6 in SIN3L complex – Cryo EM
    
• HDAC class IIA
• HDAC4
  • 2h8n – hHDAC4 N terminal
    
  • 2o94 - hHDAC4 N terminal (mutant)
    
  • 2vqw - hHDAC4 catalytic domain (mutant)
    
  • 2vqj, 2vqm, 4cbt, 5a2s – hHDAC4 catalytic domain + inhibitor
    
  • 6fyz - hHDAC4 catalytic domain + SAHA derivative
    
  • 2vqo, 2vqq, 2vqv, 4cby – hHDAC4 catalytic domain (mutant) + inhibitor
    
  • 5zop, 5zoo - hHDAC4 catalytic domain (mutant) + SMRT corepressor
    
• HDAC5
  • 5uwi – hHDAC5 + RAN + RANBP1 + exportin
    
• HDAC7
  • 3c0y – hHDAC7 catalytic domain
    
  • 3c0z - hHDAC7 catalytic domain + octanedioic acid hydroxyamide phenylamide
    
  • 3c10 - hHDAC7 catalytic domain + trichostatin A
    
  • 3znr, 3zns - hHDAC7 catalytic domain + inhibitor
    
  • 8wzl – AtHDAC7 8-383
    
• HDAC9
  • 1tqe – mHDAC9 + myocyte-specific enhancer factor + DNA – mouse
• HDAC10 or polyamine deacetylase 10
  • 5td7, 7kuv – zHDAC10 - zebrafish
    
  • 6ufn, 6ufo, 6uhu, 6uhv, 6uii, 6uij, 6uil, 6uim, 6wbq, 6wdv, 6wdw, 6wdx, 6wdy, 7sgg, 7sgi, 7sgj, 7sgk, 7u3m, 7u59, 7u69, 7u6a, 7u6b, 9cbf, 9cbg, 9cbh, 9cbi – zHDAC10 + inhibitor
    
  • 6vnq, 7kuq, 7kur, 7kus, 7kut – zHDAC10 (mutant) + inhibitor
    
• HDAC
  • 4a6q, 4a90 - hHDAC subunit SAP18
    
  • 2hde – hHDAC subunit SAP18 (mutant) – NMR
    
  • 4a8x - hHDAC subunit SAP18 + RNA-binding protein + hook-like
    
  • 2kdp – hHDAC subunit SAP30 – NMR
    
  • 2ld7 – hHDAC subunit SAP30 +SIN3A PAH 3 domain – NMR
    
  • 5ikk – HDAC CLR3 – fission yeast
    
  • 7q1b, 7q1c – HDAC DAC2 + inhibitor – Trypanosoma cruzi
    
  • 9gky – VcHDAC + decanoic acid – Vibrio cholerae
    
  • 9gkv – VcHDAC + SAHA
    
• HDAC class IIB
• HDAC6; ; Domains – catalytic 2 288-646; CD1 – 40-440; CD2 440-798; zinc finger 1109-1213
  • 3c5k – hHDAC6 zinc finger domain
    
  • 3gv4 - hHDAC6 zinc finger domain + ubiquitin peptide
    
  • 3phd - hHDAC6 + polyubiquitin
    
  • 5b8d, 5kh3, 5kh7, 5kh9, 6ce6, 6ce8, 6cea, 6cec, 6ced, 6cee, 6cef, 5wpb, 5wbn, 8g43, 8g44, 8g45 – hHDAC6 zinc finger + inhibitor
    
  • 7qno – zHDAC6 CD1+CD2 domain
    
  • 5eem – zHDAC6 catalytic domain
    
  • 5edu, 5eef, 5eek, 5een, 5ef7, 5ef8, 5efb, 5efg, 5efh, 5g0f, 5g0g, 5g0h, 5g0i, 5g0j, 5wgi, 5wgk, 5wgl, 5wgm, 6cgp, 6cw8, 6dvl, 6dvm, 6dvn, 6dvo, 6mr5, 6pye, 6pzo, 6pzr, 6pzs, 6pzu, 6q0z, 6r0k, 6tcy, 6thv, 6uo2, 6uo3, 6uo5, 6uo7, 6v79, 6v7a, 6vnr, 6zw1, 7jom, 7o2p, 7o2r, 7u8z, 7uk2, 8bjk, 8cj7, 8d98, 8d99, 8d9a, 8d9b, 8d9c, 8g1z, 8g20, 8gd4, 8qa7, 8tq0, 9cbj, 9cbk, 9dm6, 9efc, 9efr, 9efx, 9egf, 9egu, 9eu0, 9ggh, 9ggk, 9mqp – zHDAC6 catalytic domain 2 + inhibitor
    
  • 6uo4, 6uo7, 6uob, 6uoc, 6wyo – zHDAC6 catalytic domain (mutant) + inhibitor
    
  • 5eei, 5w5k, 6csp, 6csq, 6csr, 6css – zHDAC6 catalytic domain + SAHA derivative
    
  • 6wyp, 6wyq – zHDAC6 catalytic domain (mutant) + SAHA derivative
    
  • 6wsj, 8eqi – zHDAC6 catalytic domain 2 + peptide
    
  • 5efj – zHDAC6 catalytic domain 2 + HC toxin
    
  • 53fj, 5efk, 5efn – zHDAC6 catalytic domain (mutant) + peptide
    
  • 8a8z – zHDAC6 CD2 domain 440-798 + inhibitor
    
• HDAC15
  • 6j6t – AtHDAC15 HD domain
    
• HDAC class III
• SIRT1 or NAD-dependent protein deacetylase sirtuin-1
  • 4ig9 – hSIRT1 + Zn
    
  • 4i5i – hSIRT1 + NAD + indole + Zn
    
  • 4if6, 4kxq – hSIRT1 + ADP-ribose + Zn
    
  • 5btr – hSIRT1 + acetyl lysine peptide + resveratol + Zn
    
  • 4zzh – hSIRT1 + activator + Zn
    
  • 4zzi – hSIRT1 + activator + inhibitor + Zn
    
  • 4zzj – hSIRT1 + acetyl lysine peptide + activator + Zn
    
• SIRT2
  • 1j8f, 3zgo, 9s44 – hSIRT2 + Zn
    
  • 5yqo, 5yqn, 5yqm, 5yql – hSIRT2 + inhibitor + Zn
    
  • 5y0z – hSIRT2 (mutant) + inhibitor + Zn
    
  • 3zgv, 5d7o – hSIRT2+ ADP ribose + Zn
    
  • 4y6q – hSIRT2+ ADP ribose derivative + Zn
    
  • 4l3o, 4y6l, 4y6o – hSIRT2 + acetyl lysine peptide + Zn
    
  • 4x3o, 4x3p, 6l65, 6l66, 6l71, 7bos, 7bot – hSIRT2 + myristoyl peptide + Zn
    
  • 4rmg, 5dy4, 5dy5, 5y5n, 5mat, 6nr0 – hSIRT2 + inhibitor + Zn
    
  • 6qcn – hSIRT2 + ADP-ribose + quercetin derivative + Zn
    
  • 5d7p, 5d7q, 5mar – hSIRT2 + inhibitor + ADP-ribose + Zn
    
  • 4rmh, 4rmi – hSIRT2 + acetyl lysine peptide + inhibitor + Zn
    
  • 4r8m – hSIRT2 + peptide + tridecanethial + Zn
    
  • 4rmj – hSIRT2 + ADP-ribose + nicotinamide + Zn
    
  • 5g4c – hSIRT2 + carba-NAD + Zn
    
  • 5fyq – hSIRT2 + RAN AA peptide + Zn
    
  • 5dy5 – hSIRT2 + thiazole derivative + piperazine derivative + Zn
    
  • 5dy4 – hSIRT2 + thiazole derivative + NAD + Zn
    
  • 5d7q, 5d7p, 5d7o – hSIRT2 + oxolan derivative + Zn
    
  • 2hjh – ySIRT2 + pseudosubstrate + nicotinamide + Zn
    
  • 4iao – ySIRT2 + SIRT4 + ADP-ribose + Zn
    
• SIRT3
  • 5d7n – hSIRT3 + Zn
    
  • 3gls – hSIRT3 (mutant) + Zn
    
  • 3glu, 5y4h, 5ytk – hSIRT3 + peptide + Zn
    
  • 6iso – hSIRT3 + histone peptide + Zn
    
  • 5bwn, 5bwo – hSIRT3 + palmitoyl H3K9 peptide + Zn
    
  • 5bwl – hSIRT3 + succinyl peptide + Zn
    
  • 3glr, 3glt, 4bve, 4fvt, 6iso – hSIRT3 + acetyl lysine peptide + Zn
    
  • 4hd8 – hSIRT3 + acetyl lysine peptide + piceatannol + Zn
    
  • 4fz3 – hSIRT3 + acetyl lysine peptide + coumarine derivative + Zn
    
  • 4c78, 4c7b – hSIRT3 + acetyl lysine peptide + resveratol derivative + Zn
    
  • 5z94, 5z93, 5zgc – hSIRT3 + histone peptide + Zn
    
  • 4jsr, 4jt8, 4jt9, 4o8z – hSIRT3 + inhibitor + Zn
    
  • 4gbn5 – hSIRT3 + inhibitor + carba-NAD + Zn
    
  • 4bv3 – hSIRT3 + inhibitor + NAD + ADP-ribose + Zn
    
  • 4bvb, 4bvh – hSIRT3 + inhibitor + ADP-ribose + Zn
    
  • 4bvf, 4bvg – hSIRT3 + acetyl lysine peptide + inhibitor + Zn
    
  • 5h4d – hSIRT3 + agonist + NAD + Zn
    
• SIRT4
  • 5ojn – hSIRT4 + ADP-ribose + Zn – Xenopus tropicalis
    
• SIRT5
  • 2b4y, 4bn4 – hSIRT5 + ADP-ribose + Zn
    
  • 2nyr, 5xhs – hSIRT5 + inhibitor + Zn
    
  • 6ljk, 6ljm, 6ljn – hSIRT5 + peptide substrate + Zn
    
  • 3rig, 3riy, 4f4u – hSIRT5 + acetyl lysine peptide + Zn
    
  • 4gic – hSIRT5 + acetyl lysine peptide + carba-NAD + Zn
    
  • 4f56 – hSIRT5 + peptide + intermediate + Zn
    
  • 4hda – hSIRT5 + acetyl lysine peptide + resveratrol + Zn
    
  • 6ace, 6acl, 6aco, 6acp – hSIRT5 + succinyl peptide + Zn
    
  • 4utn, 4utr, 4utv, 4utx, 4utz, 4uu7, 4uu8, 4uua, 4uub, 6fkz, 6fky, 6flg – zSIRT5 + acetyl lysine peptide + inhibitor + Zn
    
  • 6enx, 6eo0, 6eqs – zSIRT5 + inhibitor + Zn
    
  • 5ojo – zSIRT5 + CPS1 peptide + Zn
    
• SIRT6
  • 3k35, 6xuy, 6xv6 – hSIRT6 + ADP-ribose + Zn
    
  • 5x16 – hSIRT6 + oxolan derivative + Zn
    
  • 6hoy – hSIRT6 + ADP-ribose + trichostatin + Zn
    
  • 6qcd, 6qce, 6qch, 6qcj – hSIRT6 + ADP-ribose + quercetin derivative + Zn
    
  • 3pki, 3pkj – hSIRT6 (mutant) + ADP-ribose derivative + Zn
    
  • 3zg6 – hSIRT6 + acetyl lysine peptide + ADP-ribose + Zn
    
  • 5mfz, 5mfp, 5mf6, 5mgn, 6xv1, 6xvg, 6zu4 – hSIRT6 + activator + Zn
    
  • 5y2f, 7cl0, 7cl1 – hSIRT6 + peptide activator + Zn
    
• SIRT7
  • 5iqz – hSIRT7 N-terminal
    
• HDAC-like
  • 1zz0, 5g1b – AbHDAH – Alcalifenaceae bacterium
    
  • 1zz3, 2gh6, 2vcg, 5g1a, 5g1c, 5g3w – AbHDAH + inhibitor
    
  • 5g17 – AbHDAH (mutant) + inhibitor
    
  • 1zz1 – AbHDAH + SAHA
    
  • 5g0y – PaHDAH – Pseudomonas aeruginosa
    
  • 5li3 – PaHDAH + inhibitor
    

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Michal Harel, Openfox