Histone deacetylase 6
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 1109–1213 | Not recorded | ZN ZINC ION × 3 EYM 3-(4-methyl-3-oxo-3,4-dihydroquinoxalin-2-yl)propanoic acid × 1 UNX UNKNOWN LIGAND × 4 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol | Resolution 1.55 Å R-free 0.169 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 6CEE | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 3C5K Crystal structure of human HDAC6 zinc finger domain Deposited 2008-01-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1109–1215（107 aa）
Fragment：Residues 1109-1215
|
Not recorded | ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；297 K；3.5M Na formate, 100mM Bis-tris propane pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K
|
Resolution 1.55 Å R-free 0.227 |
| 3GV4 Crystal structure of human HDAC6 zinc finger domain and ubiquitin C-terminal peptide RLRGG Deposited 2009-03-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1109–1215（107 aa）
Fragment：UNP residues 1109-1215
|
Not recorded | ZN ZINC ION × 3 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；297 K；20% PEG3350, 0.2 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 297K
|
Resolution 1.72 Å R-free 0.230 |
| 3PHD Crystal structure of human HDAC6 in complex with ubiquitin Deposited 2010-11-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1109–1215（107 aa）
Chain B
1109–1215（107 aa）
Chain C
1109–1215（107 aa）
Chain D
1109–1215（107 aa）
|
Not recorded | ZN ZINC ION × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.6；297 K；15% PEG 3350, 0.1M Ammonium Sulphate, 0.1M Bis-Tris, pH 5.6, temperature 297K
|
Resolution 3.00 Å R-free 0.265 |
| 5B8D Crystal structure of a low occupancy fragment candidate (N-(4-Methyl-1,3-thiazol-2-yl)propanamide) bound adjacent to the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2016-06-14 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1109–1213（105 aa）
|
Not recorded | ZN ZINC ION × 3 FMT FORMIC ACID × 2 6T4 ~{N}-(4-methyl-1,3-thiazol-2-yl)ethanamide × 1 UNX UNKNOWN LIGAND × 36 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol
|
Resolution 1.05 Å R-free 0.146 |
| 5EDU Crystal structure of human histone deacetylase 6 catalytic domain 2 in complex with trichostatin A Deposited 2015-10-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
479–835（357 aa）
Fragment：MBP + HD6 catalytic domain 2 (UNP residues 479-835)
|
Not recorded | TSN TRICHOSTATIN A × 1 ZN ZINC ION × 1 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M potassium sodium tartrate, 20% PEG3350
|
Resolution 2.79 Å R-free 0.275 |
| 5EDU Crystal structure of human histone deacetylase 6 catalytic domain 2 in complex with trichostatin A Deposited 2015-10-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
479–835（357 aa）
Fragment：MBP + HD6 catalytic domain 2 (UNP residues 479-835)
|
Not recorded | TSN TRICHOSTATIN A × 1 ZN ZINC ION × 1 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M potassium sodium tartrate, 20% PEG3350
|
Resolution 2.79 Å R-free 0.275 |
| 5KH3 Crystal structure of fragment (3-(5-Chloro-1,3-benzothiazol-2-yl)propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2016-06-14 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1109–1213（105 aa）
|
Not recorded | ZN ZINC ION × 3 UNX UNKNOWN LIGAND × 13 6U6 3-(5-chloranyl-1,3-benzothiazol-2-yl)propanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol
|
Resolution 1.60 Å R-free 0.191 |
| 5KH7 Crystal structure of fragment (3-[6-Oxo-3-(3-pyridinyl)-1(6H)-pyridazinyl]propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2016-06-14 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1109–1213（105 aa）
|
Not recorded | ZN ZINC ION × 3 6T7 3-(6-oxidanylidene-3-pyridin-3-yl-pyridazin-1-yl)propanoic acid × 1 UNX UNKNOWN LIGAND × 15 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol
|
Resolution 1.70 Å R-free 0.183 |
| 5KH9 Crystal structure of a low occupancy fragment candidate (5-[(4-Isopropylphenyl)amino]-6-methyl-1,2,4-triazin-3(2H)-one) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2016-06-14 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1109–1213（105 aa）
|
Not recorded | ZN ZINC ION × 3 FMT FORMIC ACID × 1 6T5 6-methyl-5-[(4-propan-2-ylphenyl)amino]-2~{H}-1,2,4-triazin-3-one × 1 UNX UNKNOWN LIGAND × 33 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol
|
Resolution 1.07 Å R-free 0.150 |
| 5WBN Crystal structure of fragment 3-(3-Benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2017-06-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1108–1213（106 aa）
|
Not recorded | ZN ZINC ION × 3 9ZV 3-(3-benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid × 1 UNX UNKNOWN LIGAND × 8 FMT FORMIC ACID × 3 CL CHLORIDE ION × 1 ACT ACETATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol
|
Resolution 1.64 Å R-free 0.168 |
| 5WPB Crystal structure of fragment 3-(3-(pyridin-2-ylmethoxy)quinoxalin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2017-08-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
957–1056（100 aa）
|
Not recorded | ZN ZINC ION × 3 B8P 3-{3-[(pyridin-2-yl)methoxy]quinoxalin-2-yl}propanoic acid × 1 UNX UNKNOWN LIGAND × 17 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol
|
Resolution 1.55 Å R-free 0.162 |
| 6CE6 Structure of HDAC6 zinc-finger ubiquitin binding domain soaked with 3,3'-(benzo[1,2-d:5,4-d']bis(thiazole)-2,6-diyl)dipropionic acid Deposited 2018-02-11 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1109–1213（105 aa）
|
Not recorded | ZN ZINC ION × 3 UNX UNKNOWN LIGAND × 3 EYP 3,3'-(benzo[1,2-d:5,4-d']bis[1,3]thiazole-2,6-diyl)dipropanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol
|
Resolution 1.60 Å R-free 0.196 |
| 6CE8 Crystal structure of fragment 2-(Benzo[d]thiazol-2-yl)acetic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2018-02-11 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1109–1213（105 aa）
|
Not recorded | ZN ZINC ION × 3 UNX UNKNOWN LIGAND × 4 EYV (1,3-benzothiazol-2-yl)acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol
|
Resolution 1.55 Å R-free 0.168 |
| 6CEA Crystal structure of fragment 3-(quinolin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2018-02-11 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1109–1213（105 aa）
|
Not recorded | ZN ZINC ION × 3 UNX UNKNOWN LIGAND × 3 EYY 3-(quinolin-2-yl)propanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol
|
Resolution 1.60 Å R-free 0.198 |
| 6CEC Crystal structure of fragment 3-(3-Methoxy-2-quinoxalinyl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2018-02-11 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1109–1213（105 aa）
|
Not recorded | ZN ZINC ION × 3 UNX UNKNOWN LIGAND × 5 EY7 3-(3-methoxyquinoxalin-2-yl)propanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol
|
Resolution 1.55 Å R-free 0.186 |
| 6CED Crystal structure of fragment 3-(3-Methyl-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2018-02-11 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1109–1213（105 aa）
|
Not recorded | ZN ZINC ION × 3 EYA 3-(3-methyl-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid × 1 UNX UNKNOWN LIGAND × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol
|
Resolution 1.70 Å R-free 0.191 |
| 6CEF Crystal structure of fragment 3-(1,3-Benzothiazol-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain Deposited 2018-02-11 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1109–1213（105 aa）
|
Not recorded | ZN ZINC ION × 3 UNX UNKNOWN LIGAND × 3 EYJ 3-(1,3-benzothiazol-2-yl)propanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol
|
Resolution 1.80 Å R-free 0.181 |
| 7ZYU HDAC6 ZnF domain inhibitor - DARPin (Designed Ankyrin repeat protein) F10 Deposited 2022-05-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1108–1215（108 aa）
|
Not recorded | ZN ZINC ION × 3 EDO 1,2-ETHANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；3.6 M sodium formate, Bis-Tris 0.1M pH=6.7, 10% w/v Glycerol, 30% w/v 1,8-Diaminooctane(additive).
|
Resolution 2.43 Å R-free 0.250 |
| 8G43 Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with 3-(3-(2-(methylamino)-2-oxoethyl)-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid Deposited 2023-02-08 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1109–1213（105 aa）
|
Not recorded | ZN ZINC ION × 3 ZU6 3-{3-[2-(methylamino)-2-oxoethyl]-4-oxo-3,4-dihydroquinazolin-2-yl}propanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；2 M sodium formate, 0.2 M sodium acetate pH4.6, 5 % ethylene glycol
|
Resolution 1.55 Å R-free 0.177 |
| 8G44 Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with 3-(3-(2-(benzylamino)-2-oxoethyl)-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid Deposited 2023-02-08 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1109–1213（105 aa）
|
Not recorded | ZN ZINC ION × 3 ZU9 3-{3-[2-(benzylamino)-2-oxoethyl]-4-oxo-3,4-dihydroquinazolin-2-yl}propanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；2 M sodium formate, 0.2 M sodium acetate pH4.6, 5 % ethylene glycol
|
Resolution 1.55 Å R-free 0.193 |
| 8G45 Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with SGC-UBD253 chemical probe Deposited 2023-02-08 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1109–1213（105 aa）
|
Not recorded | ZN ZINC ION × 3 ZUE 3-[8-chloro-3-(2-{[(2-methoxyphenyl)methyl]amino}-2-oxoethyl)-4-oxo-3,4-dihydroquinazolin-2-yl]propanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；2 M sodium formate, 0.2 M sodium acetate pH4.6, 5 % ethylene glycol
|
Resolution 1.62 Å R-free 0.190 |
20 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | HDAC6_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 3–107； UniProt 1109–1213 |