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6g3o

Crystal structure of human HDAC2 in complex with (R)-6-[3,4-Dioxo-2-(4-trifluoromethoxy-phenylamino)-cyclobut-1-enylamino]-heptanoic acid hydroxyamide

Method: X-RAY DIFFRACTION Dmax: 108.7 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone deacetylase 2

Homo sapiens

UniProt Q92769

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 7–376 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 7–376 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 7–376 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

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 6G3O 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 construct Different ligand/ion Different experimental conditions 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 construct Different ligand/ion Different experimental conditions 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 construct Different ligand/ion Different experimental conditions 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
4LY1 Structure of Human HDAC2 in complex with inhibitor 4-(acetylamino)-N-[2-amino-5-(thiophen-2-yl)phenyl]benzamide Deposited 2013-07-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 8–376（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 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
4LY1 Structure of Human HDAC2 in complex with inhibitor 4-(acetylamino)-N-[2-amino-5-(thiophen-2-yl)phenyl]benzamide Deposited 2013-07-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 8–376（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 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
4LY1 Structure of Human HDAC2 in complex with inhibitor 4-(acetylamino)-N-[2-amino-5-(thiophen-2-yl)phenyl]benzamide Deposited 2013-07-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 8–376（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 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
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
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 1–370； UniProt 7–376 Author chain B； PDBConstruct 1–370； UniProt 7–376 Author chain C； PDBConstruct 1–370； UniProt 7–376

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6g3o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6g3o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6g3o
Deposition date deposition_date2018-03-26
Structure title titleCrystal structure of human HDAC2 in complex with (R)-6-[3,4-Dioxo-2-(4-trifluoromethoxy-phenylamino)-cyclobut-1-enylamino]-heptanoic acid hydroxyamide
Keywords keywordsHDAC inhibitors, Squaramide, HISTONE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.69 Å
Radius of gyration Rg (electron density) rg_electron34.14 Å
Forward intensity I(0) i0251623000.00
Molecular weight molecular_weight127790.0 kDa
Excluded volume excluded_volume159380 ų
Envelope volume envelope_volume192330 ų
Hydration-shell volume shell_volume46511 ų
Envelope diameter envelope_diameter111.3 Å
Shell Rg shell_rg41.00 Å
Envelope Rg envelope_rg34.07 Å
Shape Rg shape_rg34.15 Å
Total Rg total_rg34.56 Å
Total atoms total_atoms8963
Residues n_residues1101
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax108.7 Å
Rg (real space) rg_real34.58 Å
Rg uncertainty (real space) rg_real_error0.70 Å
I(0) (real space) i0_real2.5160e+08
I(0) uncertainty (real space) i0_real_error4.3920e+06
Rg (reciprocal space) rg_reciprocal34.65 Å
I(0) (reciprocal space) i0_reciprocal251600000.0000
Solution quality estimate total_estimate0.9081
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.8 Å
Skewness Skewness skewness0.140
Kurtosis Kurtosis kurtosis-0.707
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha85430000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.955
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id6g3oA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily20 — Histone deacetylase domain
Domain ID domain_id6g3oB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily20 — Histone deacetylase domain
Domain ID domain_id6g3oC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily20 — Histone deacetylase domain
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8. Citations (1)

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9. Files and Curves (10)