Histone deacetylase 2
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 8–376 | Fragment：core domain (UNP residues 8-376) | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 PG4 TETRAETHYLENE GLYCOL × 3 20Y 4-(acetylamino)-N-[2-amino-5-(thiophen-2-yl)phenyl]benzamide × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.1M CHES, pH 9.5, 40% PEG-600, VAPOR DIFFUSION, SITTING DROP, temperature 293K | Resolution 1.57 Å R-free 0.187 |
| 2 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain B； UniProt 8–376 | Fragment：core domain (UNP residues 8-376) | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 PG4 TETRAETHYLENE GLYCOL × 3 20Y 4-(acetylamino)-N-[2-amino-5-(thiophen-2-yl)phenyl]benzamide × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.1M CHES, pH 9.5, 40% PEG-600, VAPOR DIFFUSION, SITTING DROP, temperature 293K | Resolution 1.57 Å R-free 0.187 |
| 3 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain C； UniProt 8–376 | Fragment：core domain (UNP residues 8-376) | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 PG4 TETRAETHYLENE GLYCOL × 2 20Y 4-(acetylamino)-N-[2-amino-5-(thiophen-2-yl)phenyl]benzamide × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.1M CHES, pH 9.5, 40% PEG-600, VAPOR DIFFUSION, SITTING DROP, temperature 293K | Resolution 1.57 Å R-free 0.187 |
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 4LY1 | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 3MAX Crystal Structure of Human HDAC2 complexed with an N-(2-aminophenyl)benzamide Deposited 2010-03-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
9–374（366 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 LLX N-(4-aminobiphenyl-3-yl)benzamide × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9.5；298 K；40% (v/v) PEG-600, 0.1 mM CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.05 Å R-free 0.204 |
| 3MAX Crystal Structure of Human HDAC2 complexed with an N-(2-aminophenyl)benzamide Deposited 2010-03-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
9–374（366 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 LLX N-(4-aminobiphenyl-3-yl)benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9.5；298 K；40% (v/v) PEG-600, 0.1 mM CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.05 Å R-free 0.204 |
| 3MAX Crystal Structure of Human HDAC2 complexed with an N-(2-aminophenyl)benzamide Deposited 2010-03-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
9–374（366 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 LLX N-(4-aminobiphenyl-3-yl)benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9.5；298 K；40% (v/v) PEG-600, 0.1 mM CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.05 Å R-free 0.204 |
| 4LXZ Structure of Human HDAC2 in complex with SAHA (vorinostat) Deposited 2013-07-30 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
8–376（369 aa）
Fragment：core domain (UNP residues 8-376)
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 PG4 TETRAETHYLENE GLYCOL × 3 SHH OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.1M CHES, pH 9.5, 40% PEG-600, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.85 Å R-free 0.192 |
| 4LXZ Structure of Human HDAC2 in complex with SAHA (vorinostat) Deposited 2013-07-30 | Different ligand/ion Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
8–376（369 aa）
Fragment：core domain (UNP residues 8-376)
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 PG4 TETRAETHYLENE GLYCOL × 3 SHH OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.1M CHES, pH 9.5, 40% PEG-600, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.85 Å R-free 0.192 |
| 4LXZ Structure of Human HDAC2 in complex with SAHA (vorinostat) Deposited 2013-07-30 | Different ligand/ion Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
8–376（369 aa）
Fragment：core domain (UNP residues 8-376)
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 PG4 TETRAETHYLENE GLYCOL × 2 SHH OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.1M CHES, pH 9.5, 40% PEG-600, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.85 Å R-free 0.192 |
| 5IWG HDAC2 WITH LIGAND BRD4884 Deposited 2016-03-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
8–375（368 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 IWX N-(4-amino-4'-fluoro[1,1'-biphenyl]-3-yl)oxane-4-carboxamide × 1 PG5 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE × 1 PGE TRIETHYLENE GLYCOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG 400, potassium phosphate
|
Resolution 1.66 Å R-free 0.208 |
| 5IWG HDAC2 WITH LIGAND BRD4884 Deposited 2016-03-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
8–375（368 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 IWX N-(4-amino-4'-fluoro[1,1'-biphenyl]-3-yl)oxane-4-carboxamide × 1 PEG DI(HYDROXYETHYL)ETHER × 3 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG 400, potassium phosphate
|
Resolution 1.66 Å R-free 0.208 |
| 5IWG HDAC2 WITH LIGAND BRD4884 Deposited 2016-03-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
8–375（368 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 IWX N-(4-amino-4'-fluoro[1,1'-biphenyl]-3-yl)oxane-4-carboxamide × 1 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG 400, potassium phosphate
|
Resolution 1.66 Å R-free 0.208 |
| 5IX0 HDAC2 WITH LIGAND BRD7232 Deposited 2016-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
7–375（369 aa）
Fragment：UNP residues 7-375
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 6EZ (3-exo)-N-(4-amino-4'-fluoro[1,1'-biphenyl]-3-yl)-8-oxabicyclo[3.2.1]octane-3-carboxamide × 1 PEG DI(HYDROXYETHYL)ETHER × 2 PG4 TETRAETHYLENE GLYCOL × 1 PG5 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE × 1 PGE TRIETHYLENE GLYCOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；PEG 400, potassium phosphate
|
Resolution 1.72 Å R-free 0.200 |
| 5IX0 HDAC2 WITH LIGAND BRD7232 Deposited 2016-03-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
7–375（369 aa）
Fragment：UNP residues 7-375
Chain B
7–375（369 aa）
Fragment：UNP residues 7-375
Chain C
7–375（369 aa）
Fragment：UNP residues 7-375
|
Not recorded | ZN ZINC ION × 3 CA CALCIUM ION × 6 6EZ (3-exo)-N-(4-amino-4'-fluoro[1,1'-biphenyl]-3-yl)-8-oxabicyclo[3.2.1]octane-3-carboxamide × 3 PEG DI(HYDROXYETHYL)ETHER × 5 PG4 TETRAETHYLENE GLYCOL × 2 PG5 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE × 3 PGE TRIETHYLENE GLYCOL × 9 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；PEG 400, potassium phosphate
|
Resolution 1.72 Å R-free 0.200 |
| 5IX0 HDAC2 WITH LIGAND BRD7232 Deposited 2016-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
7–375（369 aa）
Fragment：UNP residues 7-375
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 6EZ (3-exo)-N-(4-amino-4'-fluoro[1,1'-biphenyl]-3-yl)-8-oxabicyclo[3.2.1]octane-3-carboxamide × 1 PEG DI(HYDROXYETHYL)ETHER × 2 PG5 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE × 2 PGE TRIETHYLENE GLYCOL × 5 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；PEG 400, potassium phosphate
|
Resolution 1.72 Å R-free 0.200 |
| 5IX0 HDAC2 WITH LIGAND BRD7232 Deposited 2016-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
7–375（369 aa）
Fragment：UNP residues 7-375
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 6EZ (3-exo)-N-(4-amino-4'-fluoro[1,1'-biphenyl]-3-yl)-8-oxabicyclo[3.2.1]octane-3-carboxamide × 1 PEG DI(HYDROXYETHYL)ETHER × 1 PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 2 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；PEG 400, potassium phosphate
|
Resolution 1.72 Å R-free 0.200 |
| 6G3O Crystal structure of human HDAC2 in complex with (R)-6-[3,4-Dioxo-2-(4-trifluoromethoxy-phenylamino)-cyclobut-1-enylamino]-heptanoic acid hydroxyamide Deposited 2018-03-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
7–376（370 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 EL8 (6~{R})-6-[[3,4-bis(oxidanylidene)-2-[[4-(trifluoromethyloxy)phenyl]amino]cyclobuten-1-yl]amino]-~{N}-oxidanyl-heptanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M TRIS, pH 9.15, 54 %(w/v) PEG 400
|
Resolution 2.27 Å R-free 0.219 |
| 6G3O Crystal structure of human HDAC2 in complex with (R)-6-[3,4-Dioxo-2-(4-trifluoromethoxy-phenylamino)-cyclobut-1-enylamino]-heptanoic acid hydroxyamide Deposited 2018-03-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
7–376（370 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 EL8 (6~{R})-6-[[3,4-bis(oxidanylidene)-2-[[4-(trifluoromethyloxy)phenyl]amino]cyclobuten-1-yl]amino]-~{N}-oxidanyl-heptanamide × 1 1PE PENTAETHYLENE GLYCOL × 1 SO4 SULFATE ION × 1 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M TRIS, pH 9.15, 54 %(w/v) PEG 400
|
Resolution 2.27 Å R-free 0.219 |
| 6G3O Crystal structure of human HDAC2 in complex with (R)-6-[3,4-Dioxo-2-(4-trifluoromethoxy-phenylamino)-cyclobut-1-enylamino]-heptanoic acid hydroxyamide Deposited 2018-03-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
7–376（370 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 EL8 (6~{R})-6-[[3,4-bis(oxidanylidene)-2-[[4-(trifluoromethyloxy)phenyl]amino]cyclobuten-1-yl]amino]-~{N}-oxidanyl-heptanamide × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M TRIS, pH 9.15, 54 %(w/v) PEG 400
|
Resolution 2.27 Å R-free 0.219 |
| 6WBW Structure of Human HDAC2 in complex with an ethyl ketone inhibitor Deposited 2020-03-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–376（376 aa）
|
Not recorded | TV1 N-{(1S)-7,7-dihydroxy-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]nonyl}-1-methylazetidine-3-carboxamide × 1 ZN ZINC ION × 1 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.46 Å R-free 0.197 |
| 6WBW Structure of Human HDAC2 in complex with an ethyl ketone inhibitor Deposited 2020-03-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–376（376 aa）
|
Not recorded | TV1 N-{(1S)-7,7-dihydroxy-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]nonyl}-1-methylazetidine-3-carboxamide × 1 ZN ZINC ION × 1 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.46 Å R-free 0.197 |
| 6WBW Structure of Human HDAC2 in complex with an ethyl ketone inhibitor Deposited 2020-03-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–376（376 aa）
|
Not recorded | TV1 N-{(1S)-7,7-dihydroxy-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]nonyl}-1-methylazetidine-3-carboxamide × 1 ZN ZINC ION × 1 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.46 Å R-free 0.197 |
| 6WBZ Structure of Human HDAC2 in complex with an ethyl ketone inhibitor containing a spiro-bicyclic group Deposited 2020-03-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 3 TV7 (1S)-N-{(1S)-7,7-dihydroxy-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]nonyl}-6-ethyl-6-azaspiro[2.5]octane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.32 Å R-free 0.192 |
| 6WBZ Structure of Human HDAC2 in complex with an ethyl ketone inhibitor containing a spiro-bicyclic group Deposited 2020-03-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 2 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 TV7 (1S)-N-{(1S)-7,7-dihydroxy-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]nonyl}-6-ethyl-6-azaspiro[2.5]octane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.32 Å R-free 0.192 |
| 6WBZ Structure of Human HDAC2 in complex with an ethyl ketone inhibitor containing a spiro-bicyclic group Deposited 2020-03-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 TV7 (1S)-N-{(1S)-7,7-dihydroxy-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]nonyl}-6-ethyl-6-azaspiro[2.5]octane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.32 Å R-free 0.192 |
| 6WHN Histone deacetylases complex with peptide macrocycles Deposited 2020-04-08 | 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
2–385（384 aa）
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 2 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 PG4 TETRAETHYLENE GLYCOL × 3 PGE TRIETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；40% (v/v) PEG600 and 100mM CHES
pH 9.5
|
Resolution 1.54 Å R-free 0.192 |
| 6WHN Histone deacetylases complex with peptide macrocycles Deposited 2020-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–385（384 aa）
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 2 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；40% (v/v) PEG600 and 100mM CHES
pH 9.5
|
Resolution 1.54 Å R-free 0.192 |
| 6WHN Histone deacetylases complex with peptide macrocycles Deposited 2020-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2–385（384 aa）
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 2 PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；40% (v/v) PEG600 and 100mM CHES
pH 9.5
|
Resolution 1.54 Å R-free 0.192 |
| 6WHO Histone deacetylases complex with peptide macrocycles Deposited 2020-04-08 | 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
2–385（384 aa）
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 2 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 2 PG4 TETRAETHYLENE GLYCOL × 2 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；40 % PEG600 and 100mM CHES pH 9.5
|
Resolution 2.20 Å R-free 0.221 |
| 6WHO Histone deacetylases complex with peptide macrocycles Deposited 2020-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–385（384 aa）
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 2 PG4 TETRAETHYLENE GLYCOL × 3 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；40 % PEG600 and 100mM CHES pH 9.5
|
Resolution 2.20 Å R-free 0.221 |
| 6WHO Histone deacetylases complex with peptide macrocycles Deposited 2020-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2–385（384 aa）
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 2 PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；40 % PEG600 and 100mM CHES pH 9.5
|
Resolution 2.20 Å R-free 0.221 |
| 6WHQ Histone deacetylases complex with peptide macrocycles Deposited 2020-04-08 | 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
2–385（384 aa）
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 2 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 PGE TRIETHYLENE GLYCOL × 2 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；40% (v/v) PEG600 and 100mM CHES pH 9.5
|
Resolution 2.35 Å R-free 0.241 |
| 6WHQ Histone deacetylases complex with peptide macrocycles Deposited 2020-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–385（384 aa）
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 2 PGE TRIETHYLENE GLYCOL × 1 PG4 TETRAETHYLENE GLYCOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；40% (v/v) PEG600 and 100mM CHES pH 9.5
|
Resolution 2.35 Å R-free 0.241 |
| 6WHQ Histone deacetylases complex with peptide macrocycles Deposited 2020-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2–385（384 aa）
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 2 PGE TRIETHYLENE GLYCOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；40% (v/v) PEG600 and 100mM CHES pH 9.5
|
Resolution 2.35 Å R-free 0.241 |
| 6WHZ Histone deacetylases complex with peptide macrocycles Deposited 2020-04-08 | 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
2–385（384 aa）
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 2 PGE TRIETHYLENE GLYCOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；40% (v/v) PEG600 and 100mM CHES pH 9.5
|
Resolution 2.90 Å R-free 0.281 |
| 6WHZ Histone deacetylases complex with peptide macrocycles Deposited 2020-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–385（384 aa）
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 2 PGE TRIETHYLENE GLYCOL × 1 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；40% (v/v) PEG600 and 100mM CHES pH 9.5
|
Resolution 2.90 Å R-free 0.281 |
| 6WHZ Histone deacetylases complex with peptide macrocycles Deposited 2020-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2–385（384 aa）
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 1 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；40% (v/v) PEG600 and 100mM CHES pH 9.5
|
Resolution 2.90 Å R-free 0.281 |
| 6WI3 Histone deacetylases complex with peptide macrocycles Deposited 2020-04-08 | 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
2–385（384 aa）
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 2 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 PGE TRIETHYLENE GLYCOL × 1 PG4 TETRAETHYLENE GLYCOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；40% (v/v) PEG600 and 100mM CHES pH 9.5
|
Resolution 2.35 Å R-free 0.254 |
| 6WI3 Histone deacetylases complex with peptide macrocycles Deposited 2020-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–385（384 aa）
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 2 PGE TRIETHYLENE GLYCOL × 1 PG4 TETRAETHYLENE GLYCOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；40% (v/v) PEG600 and 100mM CHES pH 9.5
|
Resolution 2.35 Å R-free 0.254 |
| 6WI3 Histone deacetylases complex with peptide macrocycles Deposited 2020-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2–385（384 aa）
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 2 PGE TRIETHYLENE GLYCOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；40% (v/v) PEG600 and 100mM CHES pH 9.5
|
Resolution 2.35 Å R-free 0.254 |
| 6XDM STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN ARYL KETONE INHIBITOR Deposited 2020-06-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 SO4 SULFATE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 3 V1D N-[(1S)-1-[4-(2-fluorophenyl)-1H-imidazol-2-yl]-7,7-dihydroxy-7-(1,2-oxazol-3-yl)heptyl]-1-methylazetidine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.56 Å R-free 0.189 |
| 6XDM STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN ARYL KETONE INHIBITOR Deposited 2020-06-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 SO4 SULFATE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 V1D N-[(1S)-1-[4-(2-fluorophenyl)-1H-imidazol-2-yl]-7,7-dihydroxy-7-(1,2-oxazol-3-yl)heptyl]-1-methylazetidine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.56 Å R-free 0.189 |
| 6XDM STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN ARYL KETONE INHIBITOR Deposited 2020-06-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 SO4 SULFATE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 2 V1D N-[(1S)-1-[4-(2-fluorophenyl)-1H-imidazol-2-yl]-7,7-dihydroxy-7-(1,2-oxazol-3-yl)heptyl]-1-methylazetidine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.56 Å R-free 0.189 |
| 6XEB STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH KETONE INHIBITOR (COMPOUND E) Deposited 2020-06-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 3 V1P 5-{(1S)-7,7-dihydroxy-1-[(1-methylazetidine-3-carbonyl)amino]nonyl}-2-phenyl-1H-imidazole-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.50 Å R-free 0.193 |
| 6XEB STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH KETONE INHIBITOR (COMPOUND E) Deposited 2020-06-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 2 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 V1P 5-{(1S)-7,7-dihydroxy-1-[(1-methylazetidine-3-carbonyl)amino]nonyl}-2-phenyl-1H-imidazole-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.50 Å R-free 0.193 |
| 6XEB STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH KETONE INHIBITOR (COMPOUND E) Deposited 2020-06-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 V1P 5-{(1S)-7,7-dihydroxy-1-[(1-methylazetidine-3-carbonyl)amino]nonyl}-2-phenyl-1H-imidazole-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.50 Å R-free 0.193 |
| 6XEC STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH KETONE INHIBITOR (COMPOUND O) Deposited 2020-06-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 3 V1S (1S)-N-{(1S)-1-[5-cyano-2-(4-fluorophenyl)-1H-imidazol-4-yl]-7,7-dihydroxynonyl}-6-methyl-6-azaspiro[2.5]octane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.70 Å R-free 0.203 |
| 6XEC STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH KETONE INHIBITOR (COMPOUND O) Deposited 2020-06-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 2 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 V1S (1S)-N-{(1S)-1-[5-cyano-2-(4-fluorophenyl)-1H-imidazol-4-yl]-7,7-dihydroxynonyl}-6-methyl-6-azaspiro[2.5]octane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.70 Å R-free 0.203 |
| 6XEC STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH KETONE INHIBITOR (COMPOUND O) Deposited 2020-06-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 V1S (1S)-N-{(1S)-1-[5-cyano-2-(4-fluorophenyl)-1H-imidazol-4-yl]-7,7-dihydroxynonyl}-6-methyl-6-azaspiro[2.5]octane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.70 Å R-free 0.203 |
| 7JS8 STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN ETHYL KETONE INHIBITOR CONTAINING A SPIRO-BICYCLIC GROUP (COMPOUND 22) Deposited 2020-08-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 3 VJV (1S)-N-{(1S)-7,7-dihydroxy-1-[4-(2-methylquinolin-6-yl)-1H-imidazol-2-yl]nonyl}-6-methyl-6-azaspiro[2.5]octane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.63 Å R-free 0.190 |
| 7JS8 STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN ETHYL KETONE INHIBITOR CONTAINING A SPIRO-BICYCLIC GROUP (COMPOUND 22) Deposited 2020-08-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 2 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 VJV (1S)-N-{(1S)-7,7-dihydroxy-1-[4-(2-methylquinolin-6-yl)-1H-imidazol-2-yl]nonyl}-6-methyl-6-azaspiro[2.5]octane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.63 Å R-free 0.190 |
| 7JS8 STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN ETHYL KETONE INHIBITOR CONTAINING A SPIRO-BICYCLIC GROUP (COMPOUND 22) Deposited 2020-08-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 VJV (1S)-N-{(1S)-7,7-dihydroxy-1-[4-(2-methylquinolin-6-yl)-1H-imidazol-2-yl]nonyl}-6-methyl-6-azaspiro[2.5]octane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.63 Å R-free 0.190 |
| 7KBG Structure of Human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 20) Deposited 2020-10-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 SO4 SULFATE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 3 WBA N-{(1S)-5-[(2-fluoro-6-hydroxybenzene-1-carbonyl)amino]-1-[5-(naphthalen-2-yl)-1H-imidazol-2-yl]pentyl}-1,3-thiazole-5-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.5
|
Resolution 1.26 Å R-free 0.196 |
| 7KBG Structure of Human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 20) Deposited 2020-10-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 SO4 SULFATE ION × 3 PEG DI(HYDROXYETHYL)ETHER × 2 WBA N-{(1S)-5-[(2-fluoro-6-hydroxybenzene-1-carbonyl)amino]-1-[5-(naphthalen-2-yl)-1H-imidazol-2-yl]pentyl}-1,3-thiazole-5-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.5
|
Resolution 1.26 Å R-free 0.196 |
| 7KBG Structure of Human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 20) Deposited 2020-10-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 SO4 SULFATE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 2 WBA N-{(1S)-5-[(2-fluoro-6-hydroxybenzene-1-carbonyl)amino]-1-[5-(naphthalen-2-yl)-1H-imidazol-2-yl]pentyl}-1,3-thiazole-5-carboxamide × 1 DMS DIMETHYL SULFOXIDE × 1 WBD 2,5-dichloro-1H-benzimidazole × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.5
|
Resolution 1.26 Å R-free 0.196 |
| 7KBH Structure of Human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 16) Deposited 2020-10-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 3 WB4 N-{(1S)-5-{[2-(methylsulfanyl)benzene-1-carbonyl]amino}-1-[5-(naphthalen-2-yl)-1H-imidazol-2-yl]pentyl}-1,3-thiazole-5-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 2.68 Å R-free 0.221 |
| 7KBH Structure of Human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 16) Deposited 2020-10-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 WB4 N-{(1S)-5-{[2-(methylsulfanyl)benzene-1-carbonyl]amino}-1-[5-(naphthalen-2-yl)-1H-imidazol-2-yl]pentyl}-1,3-thiazole-5-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 2.68 Å R-free 0.221 |
| 7KBH Structure of Human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 16) Deposited 2020-10-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1 WB4 N-{(1S)-5-{[2-(methylsulfanyl)benzene-1-carbonyl]amino}-1-[5-(naphthalen-2-yl)-1H-imidazol-2-yl]pentyl}-1,3-thiazole-5-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 2.68 Å R-free 0.221 |
| 7LTG STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH APICIDIN Deposited 2021-02-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 3 YED (3S,6S,9S,15aR)-9-[(2S)-butan-2-yl]-3-(6,6-dihydroxyoctyl)-6-[(1-methoxy-1H-indol-3-yl)methyl]octahydro-2H-pyrido[1,2-a][1,4,7,10]tetraazacyclododecine-1,4,7,10(3H,12H)-tetrone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.80 Å R-free 0.198 |
| 7LTG STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH APICIDIN Deposited 2021-02-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 5 YED (3S,6S,9S,15aR)-9-[(2S)-butan-2-yl]-3-(6,6-dihydroxyoctyl)-6-[(1-methoxy-1H-indol-3-yl)methyl]octahydro-2H-pyrido[1,2-a][1,4,7,10]tetraazacyclododecine-1,4,7,10(3H,12H)-tetrone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.80 Å R-free 0.198 |
| 7LTG STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH APICIDIN Deposited 2021-02-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 YED (3S,6S,9S,15aR)-9-[(2S)-butan-2-yl]-3-(6,6-dihydroxyoctyl)-6-[(1-methoxy-1H-indol-3-yl)methyl]octahydro-2H-pyrido[1,2-a][1,4,7,10]tetraazacyclododecine-1,4,7,10(3H,12H)-tetrone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.80 Å R-free 0.198 |
| 7LTK STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN INHIBITOR THAT LACKS A ZINC BINDING GROUP (COMPOUND 12) Deposited 2021-02-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 ACT ACETATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 3 YEM N-{(1S)-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]pentyl}-1-methylazetidine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.59 Å R-free 0.198 |
| 7LTK STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN INHIBITOR THAT LACKS A ZINC BINDING GROUP (COMPOUND 12) Deposited 2021-02-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 ACT ACETATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2 YEM N-{(1S)-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]pentyl}-1-methylazetidine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.59 Å R-free 0.198 |
| 7LTK STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN INHIBITOR THAT LACKS A ZINC BINDING GROUP (COMPOUND 12) Deposited 2021-02-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 ACT ACETATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 YEM N-{(1S)-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]pentyl}-1-methylazetidine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.59 Å R-free 0.198 |
| 7LTL STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN INHIBITOR LACKING A ZINC BINDING GROUP (COMPOUND 19) Deposited 2021-02-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 ACT ACETATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 3 YEV (2R)-2-(5-hydroxy-2-methyl-1H-indol-3-yl)-N-{(1S)-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]pentyl}propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.49 Å R-free 0.195 |
| 7LTL STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN INHIBITOR LACKING A ZINC BINDING GROUP (COMPOUND 19) Deposited 2021-02-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 3 CA CALCIUM ION × 2 ACT ACETATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2 YEV (2R)-2-(5-hydroxy-2-methyl-1H-indol-3-yl)-N-{(1S)-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]pentyl}propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.49 Å R-free 0.195 |
| 7LTL STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN INHIBITOR LACKING A ZINC BINDING GROUP (COMPOUND 19) Deposited 2021-02-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 5 CA CALCIUM ION × 2 ACT ACETATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 YEV (2R)-2-(5-hydroxy-2-methyl-1H-indol-3-yl)-N-{(1S)-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]pentyl}propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.49 Å R-free 0.195 |
| 7MOS Structure of HDAC2 in complex with a macrocyclic inhibitor (compound 4) Deposited 2021-05-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 5 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 3 ZLV (3S,18S,20aR)-18-(6,6-dihydroxyoctyl)-1,5,6,7,8,18,19,20a-octahydro-4H-14,17-epiminoazeto[1,2-g][1,7,10,13]benzoxatriazacycloheptadecin-20(2H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.70 Å R-free 0.208 |
| 7MOS Structure of HDAC2 in complex with a macrocyclic inhibitor (compound 4) Deposited 2021-05-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 ZLV (3S,18S,20aR)-18-(6,6-dihydroxyoctyl)-1,5,6,7,8,18,19,20a-octahydro-4H-14,17-epiminoazeto[1,2-g][1,7,10,13]benzoxatriazacycloheptadecin-20(2H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.70 Å R-free 0.208 |
| 7MOS Structure of HDAC2 in complex with a macrocyclic inhibitor (compound 4) Deposited 2021-05-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 ZLV (3S,18S,20aR)-18-(6,6-dihydroxyoctyl)-1,5,6,7,8,18,19,20a-octahydro-4H-14,17-epiminoazeto[1,2-g][1,7,10,13]benzoxatriazacycloheptadecin-20(2H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.70 Å R-free 0.208 |
| 7MOT Structure of HDAC2 in complex with an inhibitor (compound 9) Deposited 2021-05-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 3 V1P 5-{(1S)-7,7-dihydroxy-1-[(1-methylazetidine-3-carbonyl)amino]nonyl}-2-phenyl-1H-imidazole-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.54 Å R-free 0.203 |
| 7MOT Structure of HDAC2 in complex with an inhibitor (compound 9) Deposited 2021-05-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 2 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 V1P 5-{(1S)-7,7-dihydroxy-1-[(1-methylazetidine-3-carbonyl)amino]nonyl}-2-phenyl-1H-imidazole-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.54 Å R-free 0.203 |
| 7MOT Structure of HDAC2 in complex with an inhibitor (compound 9) Deposited 2021-05-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 V1P 5-{(1S)-7,7-dihydroxy-1-[(1-methylazetidine-3-carbonyl)amino]nonyl}-2-phenyl-1H-imidazole-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.54 Å R-free 0.203 |
| 7MOX Structure of HDAC2 in complex with an inhibitor (compound 14) Deposited 2021-05-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 3 ZLS (1S)-N-[(1S)-7,7-dihydroxy-1-{4-[(1R,4S)-1,2,3,4-tetrahydro-1,4-methanonaphthalen-6-yl]-1H-imidazol-2-yl}nonyl]-6-methyl-6-azaspiro[2.5]octane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.69 Å R-free 0.202 |
| 7MOX Structure of HDAC2 in complex with an inhibitor (compound 14) Deposited 2021-05-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 2 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 ZLS (1S)-N-[(1S)-7,7-dihydroxy-1-{4-[(1R,4S)-1,2,3,4-tetrahydro-1,4-methanonaphthalen-6-yl]-1H-imidazol-2-yl}nonyl]-6-methyl-6-azaspiro[2.5]octane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.69 Å R-free 0.202 |
| 7MOX Structure of HDAC2 in complex with an inhibitor (compound 14) Deposited 2021-05-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 ZLS (1S)-N-[(1S)-7,7-dihydroxy-1-{4-[(1R,4S)-1,2,3,4-tetrahydro-1,4-methanonaphthalen-6-yl]-1H-imidazol-2-yl}nonyl]-6-methyl-6-azaspiro[2.5]octane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.69 Å R-free 0.202 |
| 7MOY Structure of HDAC2 in complex with an inhibitor (compound 19) Deposited 2021-05-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 3 ZLM (1S)-6-ethyl-N-{(1S)-1-[5-(2-ethyl-1-oxo-1,2-dihydroisoquinolin-6-yl)-1H-imidazol-2-yl]-7,7-dihydroxynonyl}-6-azaspiro[2.5]octane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.78 Å R-free 0.208 |
| 7MOY Structure of HDAC2 in complex with an inhibitor (compound 19) Deposited 2021-05-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 2 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 ZLM (1S)-6-ethyl-N-{(1S)-1-[5-(2-ethyl-1-oxo-1,2-dihydroisoquinolin-6-yl)-1H-imidazol-2-yl]-7,7-dihydroxynonyl}-6-azaspiro[2.5]octane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.78 Å R-free 0.208 |
| 7MOY Structure of HDAC2 in complex with an inhibitor (compound 19) Deposited 2021-05-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 ZLM (1S)-6-ethyl-N-{(1S)-1-[5-(2-ethyl-1-oxo-1,2-dihydroisoquinolin-6-yl)-1H-imidazol-2-yl]-7,7-dihydroxynonyl}-6-azaspiro[2.5]octane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.78 Å R-free 0.208 |
| 7MOZ Structure of HDAC2 in complex with a macrocyclic inhibitor (compound 25) Deposited 2021-05-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 3 ZL4 (1R,3S,6S,18R,27R)-6-(6,6-dihydroxyoctyl)-5,8,18,27,34-pentaazahexacyclo[25.2.2.1~7,10~.1~11,15~.1~14,18~.0~1,3~]tetratriaconta-7,9,11(33),12,14,16-hexaene-4,32-dione (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.54 Å R-free 0.201 |
| 7MOZ Structure of HDAC2 in complex with a macrocyclic inhibitor (compound 25) Deposited 2021-05-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 2 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 ZL4 (1R,3S,6S,18R,27R)-6-(6,6-dihydroxyoctyl)-5,8,18,27,34-pentaazahexacyclo[25.2.2.1~7,10~.1~11,15~.1~14,18~.0~1,3~]tetratriaconta-7,9,11(33),12,14,16-hexaene-4,32-dione (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.54 Å R-free 0.201 |
| 7MOZ Structure of HDAC2 in complex with a macrocyclic inhibitor (compound 25) Deposited 2021-05-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–376（376 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 ZL4 (1R,3S,6S,18R,27R)-6-(6,6-dihydroxyoctyl)-5,8,18,27,34-pentaazahexacyclo[25.2.2.1~7,10~.1~11,15~.1~14,18~.0~1,3~]tetratriaconta-7,9,11(33),12,14,16-hexaene-4,32-dione (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
|
Resolution 1.54 Å R-free 0.201 |
| 7ZZO HDAC2 in complex with an inhibitor Deposited 2022-05-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 KIZ [(2~{R})-1-(dimethylamino)-3-(4-fluorophenyl)-1-oxidanylidene-propan-2-yl]azanium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；38% PEG 300
0.1M pH=8.8 CHES/NaOH
|
Resolution 2.00 Å R-free 0.225 |
| 7ZZO HDAC2 in complex with an inhibitor Deposited 2022-05-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 KIZ [(2~{R})-1-(dimethylamino)-3-(4-fluorophenyl)-1-oxidanylidene-propan-2-yl]azanium × 1 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 KZF 2-(cyclohexylazaniumyl)ethanesulfonate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；38% PEG 300
0.1M pH=8.8 CHES/NaOH
|
Resolution 2.00 Å R-free 0.225 |
| 7ZZO HDAC2 in complex with an inhibitor Deposited 2022-05-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 KIZ [(2~{R})-1-(dimethylamino)-3-(4-fluorophenyl)-1-oxidanylidene-propan-2-yl]azanium × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；38% PEG 300
0.1M pH=8.8 CHES/NaOH
|
Resolution 2.00 Å R-free 0.225 |
| 7ZZP Structure of HDAC2 complexed with an inhibitory ligand Deposited 2022-05-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 6 KJ6 6-methyl-4-oxidanyl-pyran-2-one × 1 2OP (2S)-2-HYDROXYPROPANOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；39% PEG 300
0.1M pH=8.4 CHES/NaOH
|
Resolution 1.52 Å R-free 0.174 |
| 7ZZP Structure of HDAC2 complexed with an inhibitory ligand Deposited 2022-05-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 PGE TRIETHYLENE GLYCOL × 3 EDO 1,2-ETHANEDIOL × 1 KJ6 6-methyl-4-oxidanyl-pyran-2-one × 2 2OP (2S)-2-HYDROXYPROPANOIC ACID × 1 PG4 TETRAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 2 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；39% PEG 300
0.1M pH=8.4 CHES/NaOH
|
Resolution 1.52 Å R-free 0.174 |
| 7ZZP Structure of HDAC2 complexed with an inhibitory ligand Deposited 2022-05-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 2 KJ6 6-methyl-4-oxidanyl-pyran-2-one × 1 2OP (2S)-2-HYDROXYPROPANOIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；39% PEG 300
0.1M pH=8.4 CHES/NaOH
|
Resolution 1.52 Å R-free 0.174 |
| 7ZZR HDAC2 in complex with inhibitory ligand Deposited 2022-05-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 4 KJN [(2~{R})-1-(dimethylamino)-1-oxidanylidene-4-phenyl-butan-2-yl]azanium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；41% PEG 300
0.1M pH=8.8 CHES/NaOH
|
Resolution 2.17 Å R-free 0.247 |
| 7ZZR HDAC2 in complex with inhibitory ligand Deposited 2022-05-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 3 KJN [(2~{R})-1-(dimethylamino)-1-oxidanylidene-4-phenyl-butan-2-yl]azanium × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；41% PEG 300
0.1M pH=8.8 CHES/NaOH
|
Resolution 2.17 Å R-free 0.247 |
| 7ZZR HDAC2 in complex with inhibitory ligand Deposited 2022-05-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 3 KJN [(2~{R})-1-(dimethylamino)-1-oxidanylidene-4-phenyl-butan-2-yl]azanium × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；41% PEG 300
0.1M pH=8.8 CHES/NaOH
|
Resolution 2.17 Å R-free 0.247 |
| 7ZZS HDAC2 complexed with an inhibitory ligand Deposited 2022-05-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 3 EDO 1,2-ETHANEDIOL × 1 SHH OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE × 1 KK0 (5~{S})-5-(4-chlorophenyl)pyrrolidin-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40% PEG 300
0.1M pH=8.6 CHES/NaOH
|
Resolution 1.88 Å R-free 0.207 |
| 7ZZS HDAC2 complexed with an inhibitory ligand Deposited 2022-05-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 5 SHH OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE × 1 KK0 (5~{S})-5-(4-chlorophenyl)pyrrolidin-2-one × 1 KZF 2-(cyclohexylazaniumyl)ethanesulfonate × 1 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40% PEG 300
0.1M pH=8.6 CHES/NaOH
|
Resolution 1.88 Å R-free 0.207 |
| 7ZZS HDAC2 complexed with an inhibitory ligand Deposited 2022-05-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 2 SHH OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE × 1 KK0 (5~{S})-5-(4-chlorophenyl)pyrrolidin-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40% PEG 300
0.1M pH=8.6 CHES/NaOH
|
Resolution 1.88 Å R-free 0.207 |
| 7ZZT Ligand binding to HDAC2 Deposited 2022-05-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2 PGE TRIETHYLENE GLYCOL × 1 KJF [(2~{R})-1-oxidanylidene-4-phenyl-1-pyrrolidin-1-yl-butan-2-yl]azanium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40% PEG 300
0.1M pH=8.6 CHES/NaOH
|
Resolution 1.56 Å R-free 0.173 |
| 7ZZT Ligand binding to HDAC2 Deposited 2022-05-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 KJF [(2~{R})-1-oxidanylidene-4-phenyl-1-pyrrolidin-1-yl-butan-2-yl]azanium × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 PG4 TETRAETHYLENE GLYCOL × 2 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40% PEG 300
0.1M pH=8.6 CHES/NaOH
|
Resolution 1.56 Å R-free 0.173 |
| 7ZZT Ligand binding to HDAC2 Deposited 2022-05-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 KJF [(2~{R})-1-oxidanylidene-4-phenyl-1-pyrrolidin-1-yl-butan-2-yl]azanium × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；40% PEG 300
0.1M pH=8.6 CHES/NaOH
|
Resolution 1.56 Å R-free 0.173 |
| 7ZZU Inhibitory Ligand binding to HDAC2 Deposited 2022-05-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–488（488 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 5 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 3 ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 KKI 2-[4-[(2~{R},4~{S})-4-phenylpyrrolidin-2-yl]carbonylpiperazin-1-yl]pyridine-3-carbonitrile × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；43% PEG 300
0.1M pH=8.8 CHES/NaOH
|
Resolution 1.85 Å R-free 0.182 |
| 7ZZU Inhibitory Ligand binding to HDAC2 Deposited 2022-05-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–488（488 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 3 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 KKI 2-[4-[(2~{R},4~{S})-4-phenylpyrrolidin-2-yl]carbonylpiperazin-1-yl]pyridine-3-carbonitrile × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；43% PEG 300
0.1M pH=8.8 CHES/NaOH
|
Resolution 1.85 Å R-free 0.182 |
| 7ZZU Inhibitory Ligand binding to HDAC2 Deposited 2022-05-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–488（488 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 KKI 2-[4-[(2~{R},4~{S})-4-phenylpyrrolidin-2-yl]carbonylpiperazin-1-yl]pyridine-3-carbonitrile × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；43% PEG 300
0.1M pH=8.8 CHES/NaOH
|
Resolution 1.85 Å R-free 0.182 |
| 7ZZW Ligand binding to HDAC2 Deposited 2022-05-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–488（488 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 3 PG4 TETRAETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 KKW [(2~{R},4~{S})-4-(3-chlorophenyl)pyrrolidin-2-yl]-(4-thieno[2,3-c]pyridin-7-ylpiperazin-1-yl)methanone × 1 KZF 2-(cyclohexylazaniumyl)ethanesulfonate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；41% PEG 300
0.1M pH=8.8 CHES/NaOH
|
Resolution 1.73 Å R-free 0.189 |
| 7ZZW Ligand binding to HDAC2 Deposited 2022-05-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–488（488 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 4 EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 KKW [(2~{R},4~{S})-4-(3-chlorophenyl)pyrrolidin-2-yl]-(4-thieno[2,3-c]pyridin-7-ylpiperazin-1-yl)methanone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；41% PEG 300
0.1M pH=8.8 CHES/NaOH
|
Resolution 1.73 Å R-free 0.189 |
| 7ZZW Ligand binding to HDAC2 Deposited 2022-05-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–488（488 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 1 PG4 TETRAETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 KKW [(2~{R},4~{S})-4-(3-chlorophenyl)pyrrolidin-2-yl]-(4-thieno[2,3-c]pyridin-7-ylpiperazin-1-yl)methanone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；41% PEG 300
0.1M pH=8.8 CHES/NaOH
|
Resolution 1.73 Å R-free 0.189 |
| 8A0B Inhibitor binding to HDAC2 Deposited 2022-05-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 KRU 1,3-dihydroisoindol-2-yl-[(2R,4S)-4-phenylpyrrolidin-1-ium-2-yl]methanone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；41% PEG 300
.1M pH=8.8 CHES/NaOH
|
Resolution 1.75 Å R-free 0.188 |
| 8A0B Inhibitor binding to HDAC2 Deposited 2022-05-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 3 KRU 1,3-dihydroisoindol-2-yl-[(2R,4S)-4-phenylpyrrolidin-1-ium-2-yl]methanone × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；41% PEG 300
.1M pH=8.8 CHES/NaOH
|
Resolution 1.75 Å R-free 0.188 |
| 8A0B Inhibitor binding to HDAC2 Deposited 2022-05-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 KRU 1,3-dihydroisoindol-2-yl-[(2R,4S)-4-phenylpyrrolidin-1-ium-2-yl]methanone × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；41% PEG 300
.1M pH=8.8 CHES/NaOH
|
Resolution 1.75 Å R-free 0.188 |
| 8BPA Cryo-EM structure of the human SIN3B histone deacetylase complex at 3.7 Angstrom Deposited 2022-11-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 5 CA CALCIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8BPB Cryo-EM structure of the human SIN3B histone deacetylase core complex at 2.8 Angstrom Deposited 2022-11-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 3 CA CALCIUM ION × 2 ACT ACETATE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8BPC Cryo-EM structure of the human SIN3B histone deacetylase core complex with SAHA at 2.8 Angstrom Deposited 2022-11-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–488（488 aa）
|
Not recorded | SHH OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE × 1 ZN ZINC ION × 3 CA CALCIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8C60 Cryo-EM structure of the human SIN3B full-length complex at 3.4 Angstrom resolution Deposited 2023-01-10 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 5 CA CALCIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9DTQ The structure of HDAC2-CoREST in complex with KBTBD4R313PRR mutant Deposited 2024-10-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
2–488（487 aa）
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.87 Å |
| 9GGL Cryo-EM structure of KBTBD4 WT-HDAC2 2:1 complex mediated by molecular glue UM171 Deposited 2024-08-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 1 A1ACV (1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl]cyclohexane-1,4-diamine × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.13 Å |
| 9GGM Cryo-EM structure of KBTBD4 P313PRR mutant-HDAC2 2:2 complex Deposited 2024-08-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–488（488 aa）
Chain D
1–488（488 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.71 Å |
| 9GGN Cryo-EM structure of KBTBD4 WT-HDAC2 2:2 complex mediated by molecular glue UM171 Deposited 2024-08-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–488（488 aa）
Chain D
1–488（488 aa）
|
Not recorded | A1ACV (1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl]cyclohexane-1,4-diamine × 2 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9I2C Cryo-EM structure of KBTBD4 WT-HDAC2-CoREST1 2:1:1 complex mediated by molecular glue UM171 Deposited 2025-01-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–488（488 aa）
|
Not recorded | A1ACV (1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl]cyclohexane-1,4-diamine × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9JV3 Structure of Human HDAC2 Deposited 2024-10-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–404（404 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 EDO 1,2-ETHANEDIOL × 4 PEG DI(HYDROXYETHYL)ETHER × 2 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M CHES pH 9.5, 35-38% (v/v) PEG 600
|
Resolution 2.57 Å R-free 0.256 |
| 9JV3 Structure of Human HDAC2 Deposited 2024-10-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–404（404 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 EDO 1,2-ETHANEDIOL × 5 PEG DI(HYDROXYETHYL)ETHER × 1 PGE TRIETHYLENE GLYCOL × 1 PG4 TETRAETHYLENE GLYCOL × 1 1PE PENTAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M CHES pH 9.5, 35-38% (v/v) PEG 600
|
Resolution 2.57 Å R-free 0.256 |
| 9JV3 Structure of Human HDAC2 Deposited 2024-10-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–404（404 aa）
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 2 EDO 1,2-ETHANEDIOL × 4 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M CHES pH 9.5, 35-38% (v/v) PEG 600
|
Resolution 2.57 Å R-free 0.256 |
| 9JWJ Structure of Human HDAC2 in complex with inhibitor N-(2-amino-5-(furan-2-yl)phenyl)-4-(1-((phenylsulfonyl)methyl)-1H-1,2,3-triazol-4-yl)benzamid Deposited 2024-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–404（404 aa）
Chain B
1–404（404 aa）
Chain C
1–404（404 aa）
|
Not recorded | ZN ZINC ION × 3 CA CALCIUM ION × 6 A1L4X N-(2-amino-5-(furan-2-yl)phenyl)-4-(1-((phenylsulfonyl)methyl)-1H-1,2,3-triazol-4-yl)benzamid × 3 EDO 1,2-ETHANEDIOL × 9 PEG DI(HYDROXYETHYL)ETHER × 5 PGE TRIETHYLENE GLYCOL × 1 PG4 TETRAETHYLENE GLYCOL × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；0.1 M CHES pH 9.5, 35-38% (v/v) PEG 600
|
Resolution 1.78 Å R-free 0.202 |
| 9K0G Structure of Human HDAC2 in complex with inhibitor N-(2-aminophenyl)-4-(1-((phenylsulfonyl)methyl)-1H-1,2,3-triazol-4-yl)benzamide Deposited 2024-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–404（404 aa）
Chain B
1–404（404 aa）
Chain C
1–404（404 aa）
|
Not recorded | ZN ZINC ION × 3 CA CALCIUM ION × 6 A1L47 N-(2-aminophenyl)-4-(1-((phenylsulfonyl)methyl)-1H-1,2,3-triazol-4-yl)benzamide × 3 EDO 1,2-ETHANEDIOL × 8 PEG DI(HYDROXYETHYL)ETHER × 5 PGE TRIETHYLENE GLYCOL × 1 GOL GLYCEROL × 1 PG4 TETRAETHYLENE GLYCOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；0.1 M CHES pH 9.5, 35-38% (v/v) PEG 600)
|
Resolution 1.62 Å R-free 0.196 |
| 9NTB Crystal structure of human HDAC2 in complex with TNG260 Deposited 2025-03-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–404（404 aa）
|
Not recorded | A1B1V (R)-N-(4-amino-4'-fluoro-[1,1'-biphenyl]-3-yl)-4-(S-methylsulfonimidoyl)benzamide × 1 ZN ZINC ION × 1 CA CALCIUM ION × 2 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 EDO 1,2-ETHANEDIOL × 11 PEG DI(HYDROXYETHYL)ETHER × 4 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 9；293 K；35% PEG 600, 100 mM CHES pH 9.0
|
Resolution 1.80 Å R-free 0.197 |
| 9NTB Crystal structure of human HDAC2 in complex with TNG260 Deposited 2025-03-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–404（404 aa）
|
Not recorded | A1B1V (R)-N-(4-amino-4'-fluoro-[1,1'-biphenyl]-3-yl)-4-(S-methylsulfonimidoyl)benzamide × 1 ZN ZINC ION × 1 CA CALCIUM ION × 2 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 EDO 1,2-ETHANEDIOL × 6 PEG DI(HYDROXYETHYL)ETHER × 5 PG4 TETRAETHYLENE GLYCOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 9；293 K；35% PEG 600, 100 mM CHES pH 9.0
|
Resolution 1.80 Å R-free 0.197 |
| 9NTB Crystal structure of human HDAC2 in complex with TNG260 Deposited 2025-03-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–404（404 aa）
|
Not recorded | A1B1V (R)-N-(4-amino-4'-fluoro-[1,1'-biphenyl]-3-yl)-4-(S-methylsulfonimidoyl)benzamide × 1 ZN ZINC ION × 1 CA CALCIUM ION × 2 EDO 1,2-ETHANEDIOL × 5 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 9；293 K；35% PEG 600, 100 mM CHES pH 9.0
|
Resolution 1.80 Å R-free 0.197 |
47 other PDB entries and 120 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | HDAC2_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–369； UniProt 8–376 Author chain B； PDBConstruct 1–369； UniProt 8–376 Author chain C； PDBConstruct 1–369； UniProt 8–376 |
