6bgy

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(2-(1-methylpyrrolidin-2-yl)ethoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid(Compound 46)

Method: X-RAY DIFFRACTION D_max: 64.8 Å Quality: GOOD

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Lysine-specific demethylase 5A,linked KDM5A JMJ domain

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 1–87 Chain A； UniProt 348–588	Not recorded	DLJ 2-[(S)-(2-chlorophenyl){2-[(2R)-1-methylpyrrolidin-2-yl]ethoxy}methyl]-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid × 1 MN MANGANESE (II) ION × 1 EDO 1,2-ETHANEDIOL × 4 DMS DIMETHYL SULFOXIDE × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.22 Å R-free 0.193

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 6BGY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2JXJ NMR structure of the ARID domain from the histone H3K4 demethylase RBP2 Deposited 2007-11-20	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 85–175（91 aa） Fragment：ARID domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；293 K；Ionic strength (raw mmCIF value) ~200 mM salt；Pressure ambient NMR sample composition 0.4 mM [U-100% 13C; U-100% 15N] protein, 50 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.4 mM [U-100% 13C; U-100% 15N] protein, 50 mM sodium phosphate, 100 mM sodium chloride, 100% D2O \| 100% D2O	Resolution not provided
2KGG Solution Structure of JARID1A C-terminal PHD finger Deposited 2009-03-11	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1609–1659（51 aa） Fragment：PHD-TYPE C-terminal ZINC FINGER	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7；293.2 K；Ionic strength (raw mmCIF value) 20 mM Sodium Phosphate；Pressure 1 NMR measurement conditions pH 7；298.2 K；Ionic strength (raw mmCIF value) 200 mM NaCl；Pressure 1 NMR sample composition 0.2-0.5 MM [U-100% 13C; U-100% 15N] JARID1A PHD FINGER 3, 5MM DTT, 1 MM ZINC CHLORIDE, 20 MM SODIUM PHHOSPHATE, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.2-0.5 MM [U-100% 15N] JARID1A PHD FINGER 3, 10 MM MOPS, 5 MM DTT, 1 MM ZINC CHLORIDE, 12 MG/ML BACTERIOPHAGE PF1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KGI Solution structure of JARID1A C-terminal PHD finger in complex with H3(1-9)K4me3 Deposited 2009-03-12	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 × 2 PDB declaration: dimeric	Chain A 1609–1659（51 aa） Fragment：PHD-TYPE C-terminal ZINC FINGER	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7；293.2 K；Ionic strength (raw mmCIF value) 20 mM SODIUM PHOSPHATE；Pressure 1 NMR measurement conditions pH 7；298.2 K；Ionic strength (raw mmCIF value) 200 mM NACL；Pressure 1 NMR sample composition 0.2-0.5 MM [U-100% 13C; U-100% 15N] JARID1A PHD FINGER 3, 0.2-0.5 MM H3(1-9)K4ME3, 5 MM DTT, 1 MM ZINC CHLORIDE, 20 MM SODIUM PHOSPHATE, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.2-0.5 MM [U-100% 15N] JARID1A PHD FINGER 3, 0.2-0.5 MM H3(1-9)K4ME3, 5 MM DTT, 1 MM ZINC CHLORIDE, 10 MM MOPS, 12 MG/ML BACTERIOPHAGE PF1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3GL6 Crystal structure of JARID1A-PHD3 complexed with H3(1-9)K4me3 peptide Deposited 2009-03-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1609–1659（51 aa） Fragment：C-terminal PHD finger	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M Hepes-Na, 10% iso-propanol, 20% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.225
5C11 Crystal Structure of Jarid1a PHD finger bound to histone H3C4me3 peptide Deposited 2015-06-12	Different construct Different mutation/modification 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 1609–1659（51 aa） Fragment：PHD finger domain, UNP residues 1609-1659	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.02 M sodium l-glutamate, 0.02 M dl-alanine, 0.02 M glycine, 0.02 M dl-lysine HCl, 0.02 M dl-serine, 0.1 M Tris, 0.1 M Bicine, PH8.5, 12.5% MPD, 12.5% PEG 1K, 12.5% PEG 3350	Resolution 2.80 Å R-free 0.279
5CEH Structure of histone lysine demethylase KDM5A in complex with selective inhibitor Deposited 2015-07-06	Different construct Different mutation/modification 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 12–797（786 aa） Fragment：UNP residues 12-797	Not recorded	NI NICKEL (II) ION × 1 ZN ZINC ION × 2 50P 7-oxo-5-phenyl-6-(propan-2-yl)-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.1 M HEPES, pH 7.3, 12% glycerol	Resolution 3.14 Å R-free 0.238
5E6H A Linked Jumonji Domain of the KDM5A Lysine Demethylase Deposited 2015-10-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；1.5 M Ammonium sulfate 100mM Tris-HCl, pH 8.5 12% glycerol	Resolution 2.24 Å R-free 0.220
5ISL Linked KDM5A Jmj Domain Bound to the Inhibitor C49 (2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid) Deposited 2016-03-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588 Chain A 348–588（241 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588	Not recorded	MMK 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid × 1 MN MANGANESE (II) ION × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.69 Å R-free 0.202
5IVB A High Resolution Structure of a Linked KDM5A Jmj Domain with Alpha-Ketoglutarate Deposited 2016-03-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588,Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588 Chain A 348–588（241 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588,Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588	Not recorded	AKG 2-OXOGLUTARIC ACID × 1 MN MANGANESE (II) ION × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.39 Å R-free 0.214
5IVC Linked KDM5A Jmj Domain Bound to the Inhibitor N3 (4'-[(2-phenylethyl)carbamoyl][2,2'-bipyridine]-4-carboxylic acid) Deposited 2016-03-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588 Chain A 348–588（241 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588	Not recorded	6E7 4'-[(2-phenylethyl)carbamoyl][2,2'-bipyridine]-4-carboxylic acid × 1 MN MANGANESE (II) ION × 1 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.57 Å R-free 0.184
5IVE Linked KDM5A Jmj Domain Bound to the Inhibitor N8 ( 5-methyl-7-oxo-6-(propan-2-yl)-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile) Deposited 2016-03-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588 Chain A 348–588（241 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588	Not recorded	6E8 5-methyl-7-oxo-6-(propan-2-yl)-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.78 Å R-free 0.205
5IVF Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-methyl-1H-imidazol-4-yl)-2-(4,4,4-trifluorobutoxy)pyrido[3,4-d]pyrimidin-4-ol Deposited 2016-03-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588 Chain A 348–588（241 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588	Not recorded	6EB 8-(1-methyl-1H-imidazol-4-yl)-2-(4,4,4-trifluorobutoxy)pyrido[3,4-d]pyrimidin-4-ol × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.68 Å R-free 0.202
5IVJ Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4-difluoropiperidin-1-yl)ethyl]-5-fluoro-1H-indazol-3-yl}amino)pyridine-4-carboxylic acid] Deposited 2016-03-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588 Chain A 348–588（241 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588	Not recorded	6ED 3-({1-[2-(4,4-difluoropiperidin-1-yl)ethyl]-5-fluoro-1H-indazol-3-yl}amino)pyridine-4-carboxylic acid × 1 MN MANGANESE (II) ION × 1 GOL GLYCEROL × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.57 Å R-free 0.189
5IVV Linked KDM5A Jmj Domain Bound to the Inhibitor N12 [3-((1-methyl-1H-pyrrolo[2,3-b]pyridin-3-yl)amino)isonicotinic acid] Deposited 2016-03-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588 Chain A 348–588（241 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588	Not recorded	6EN 3-[(1-methyl-1H-pyrrolo[2,3-b]pyridin-3-yl)amino]pyridine-4-carboxylic acid × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.85 Å R-free 0.204
5IVY Linked KDM5A Jmj Domain Bound to the Inhibitor N16 [3-(2-(4-chlorophenyl)acetamido)isonicotinic acid] Deposited 2016-03-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588 Chain A 348–588（241 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588	Not recorded	6EO 3-{[(4-chlorophenyl)acetyl]amino}pyridine-4-carboxylic acid × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.45 Å R-free 0.209
5IW0 Linked KDM5A Jmj Domain Bound to the Inhibitor N19 [2-(5-((4-chloro-2-methylbenzyl)oxy)-1H-pyrazol-1-yl)isonicotinic acid] Deposited 2016-03-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588 Chain A 348–588（241 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588	Not recorded	6EP 2-{5-[(4-chloro-2-methylphenyl)methoxy]-1H-pyrazol-1-yl}pyridine-4-carboxylic acid × 1 AKG 2-OXOGLUTARIC ACID × 1 MN MANGANESE (II) ION × 1 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.63 Å R-free 0.192
5IWF Linked KDM5A Jmj Domain Bound to the Inhibitor 2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinamid 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 1–87（87 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588 Chain A 348–588（241 aa） Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588	Not recorded	LQT 2-[[[2-[2-(dimethylamino)ethyl-ethyl-amino]-2-oxidanylidene-ethyl]amino]methyl]pyridine-4-carboxamide × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 2.29 Å R-free 0.243
5K4L Crystal structure of KDM5A in complex with a naphthyridone inhibitor Deposited 2016-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 12–797（786 aa） Fragment：UNP residues 12-797 Chain B 12–797（786 aa） Fragment：UNP residues 12-797	Not recorded	NI NICKEL (II) ION × 2 ZN ZINC ION × 4 6QN ~{N}-ethyl-4-oxidanyl-2-oxidanylidene-1~{H}-1,7-naphthyridine-3-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.3；292 K；20% PEG3350, 0.1 M HEPES, pH 7.3, and 12% glycerol	Resolution 3.18 Å R-free 0.257
5K4L Crystal structure of KDM5A in complex with a naphthyridone inhibitor Deposited 2016-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 12–797（786 aa） Fragment：UNP residues 12-797 Chain B 12–797（786 aa） Fragment：UNP residues 12-797	Not recorded	NI NICKEL (II) ION × 2 ZN ZINC ION × 4 6QN ~{N}-ethyl-4-oxidanyl-2-oxidanylidene-1~{H}-1,7-naphthyridine-3-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.3；292 K；20% PEG3350, 0.1 M HEPES, pH 7.3, and 12% glycerol	Resolution 3.18 Å R-free 0.257
5V9P Crystal structure of pyrrolidine amide inhibitor [(3S)-3-(4-bromo-1H-pyrazol-1-yl)pyrrolidin-1-yl][3-(propan-2-yl)-1H-pyrazol-5-yl]methanone (compound 35) in complex with KDM5A Deposited 2017-03-23	Different construct Different mutation/modification 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 12–797（786 aa）	Not recorded	NI NICKEL (II) ION × 1 ZN ZINC ION × 2 90S [(3S)-3-(4-bromo-1H-pyrazol-1-yl)pyrrolidin-1-yl][3-(propan-2-yl)-1H-pyrazol-5-yl]methanone × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.3；291 K；200 uM inhibitor, 20% PEG3350, 0.1 M HEPES, pH 7.3, 12% glycerol	Resolution 3.00 Å R-free 0.248
5V9T Crystal structure of selective pyrrolidine amide KDM5a inhibitor N-{(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide (compound 48) Deposited 2017-03-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 12–797（786 aa）	Not recorded	NI NICKEL (II) ION × 1 ZN ZINC ION × 2 90V N-{(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.3；291 K；200 uM inhibitor, 20% PEG3350, 0.1 M HEPES, pH 7.3, 12% glycerol	Resolution 3.05 Å R-free 0.290
5V9T Crystal structure of selective pyrrolidine amide KDM5a inhibitor N-{(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide (compound 48) Deposited 2017-03-23	Different construct Different mutation/modification 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 12–797（786 aa）	Not recorded	NI NICKEL (II) ION × 1 ZN ZINC ION × 2 90V N-{(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.3；291 K；200 uM inhibitor, 20% PEG3350, 0.1 M HEPES, pH 7.3, 12% glycerol	Resolution 3.05 Å R-free 0.290
6BGU LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(propoxy)methyl)-1H-pyrrolo[3,2-b]pyridine (Compound N9) Deposited 2017-10-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	DKP 2-[(R)-(2-chlorophenyl)(propoxy)methyl]-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid × 1 MN MANGANESE (II) ION × 1 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 4 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.68 Å R-free 0.208
6BGV LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1l2-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N40) Deposited 2017-10-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	DQG 2-{(S)-(2-chlorophenyl)[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid × 1 MN MANGANESE (II) ION × 1 GOL GLYCEROL × 4 DMS DIMETHYL SULFOXIDE × 2 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.59 Å R-free 0.184
6BGW LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(2-(4,4-difluoropiperidin-1-yl)ethoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid(Compound N41) Deposited 2017-10-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	DKS 2-{(S)-(2-chlorophenyl)[2-(4,4-difluoropiperidin-1-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid × 1 MN MANGANESE (II) ION × 1 GOL GLYCEROL × 5 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.64 Å R-free 0.213
6BGX LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)((4,4-difluorocyclohexyl)methoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid(Compound N42) Deposited 2017-10-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	DKV 2-{(S)-(2-chlorophenyl)[(4,4-difluorocyclohexyl)methoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid × 1 MN MANGANESE (II) ION × 1 GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.88 Å R-free 0.236
6BGZ LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(2-(1-methyl-1H-imidazol-2-yl)ethoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N47) Deposited 2017-10-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	DNV 2-{(S)-(2-chlorophenyl)[2-(1-methyl-1H-imidazol-2-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid × 1 MN MANGANESE (II) ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.69 Å R-free 0.197
6BH0 LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR (R)-2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1l2-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N51) Deposited 2017-10-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	DO1 2-{(R)-(2-chlorophenyl)[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid × 1 MN MANGANESE (II) ION × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.99 Å R-free 0.219
6BH1 LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR (S)-2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1l2-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N52) Deposited 2017-10-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	DQG 2-{(S)-(2-chlorophenyl)[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid × 1 MN MANGANESE (II) ION × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.93 Å R-free 0.184
6BH2 LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR (R)-N-(1-(3-isopropyl-1H-pyrazole-5-carbonyl)pyrrolidin-3-yl)cyclopropanecarboxamide (Compound N54) Deposited 2017-10-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	MN MANGANESE (II) ION × 1 GOL GLYCEROL × 2 90V N-{(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.45 Å R-free 0.205
6BH3 LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR (S)-N-(1-(3-isopropyl-1H-pyrazole-5-carbonyl)pyrrolidin-3-yl)cyclopropanecarboxamide (Compound N55) Deposited 2017-10-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	DQJ N-{(3S)-1-[5-(propan-2-yl)-1H-pyrazole-3-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide × 1 MN MANGANESE (II) ION × 1 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.70 Å R-free 0.216
6BH4 LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 5-(1-(tert-butyl)-1H-pyrazol-4-yl)-6-isopropyl-7-oxo-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile (Compound N75/CPI-48) Deposited 2017-10-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	DQS 5-(1-tert-butyl-1H-pyrazol-4-yl)-7-oxo-6-(propan-2-yl)-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile × 1 MN MANGANESE (II) ION × 1 EDO 1,2-ETHANEDIOL × 7 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 2.05 Å R-free 0.218
6BH5 LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(3-(piperidin-1-yl)propoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N48) Deposited 2017-10-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	DNY 2-{(S)-(2-chlorophenyl)[3-(piperidin-1-yl)propoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid × 1 MN MANGANESE (II) ION × 1 EDO 1,2-ETHANEDIOL × 5 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.65 Å R-free 0.216
6DQ4 LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR GSK-J1 Deposited 2018-06-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	K0I 3-[[2-pyridin-2-yl-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)pyrimidin-4-yl]amino]propanoic acid × 1 MN MANGANESE (II) ION × 1 GOL GLYCEROL × 5 SO4 SULFATE ION × 3 DMS DIMETHYL SULFOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.39 Å R-free 0.216
6DQ4 LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR GSK-J1 Deposited 2018-06-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	K0I 3-[[2-pyridin-2-yl-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)pyrimidin-4-yl]amino]propanoic acid × 2 MN MANGANESE (II) ION × 2 GOL GLYCEROL × 10 SO4 SULFATE ION × 6 DMS DIMETHYL SULFOXIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.39 Å R-free 0.216
6DQ5 LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N43 i.e. 3-((6-(4-acryloyl-1,4-diazepan-1-yl)-2-(pyridin-2-yl)pyrimidin-4-yl)amino)propanoic acid Deposited 2018-06-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	H6G N-[6-(4-acryloyl-1,4-diazepan-1-yl)-2-(pyridin-2-yl)pyrimidin-4-yl]-beta-alanine × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.89 Å R-free 0.254
6DQ5 LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N43 i.e. 3-((6-(4-acryloyl-1,4-diazepan-1-yl)-2-(pyridin-2-yl)pyrimidin-4-yl)amino)propanoic acid Deposited 2018-06-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	H6G N-[6-(4-acryloyl-1,4-diazepan-1-yl)-2-(pyridin-2-yl)pyrimidin-4-yl]-beta-alanine × 2 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.89 Å R-free 0.254
6DQ6 LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N44 i.e. 3-((2-(pyridin-2-yl)-6-(4-(vinylsulfonyl)-1,4-diazepan-1-yl)pyrimidin-4-yl)amino)propanoic acid Deposited 2018-06-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	H6J N-{6-[4-(ethenylsulfonyl)-1,4-diazepan-1-yl]-2-(pyridin-2-yl)pyrimidin-4-yl}-beta-alanine × 1 MN MANGANESE (II) ION × 1 GOL GLYCEROL × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.59 Å R-free 0.202
6DQ6 LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N44 i.e. 3-((2-(pyridin-2-yl)-6-(4-(vinylsulfonyl)-1,4-diazepan-1-yl)pyrimidin-4-yl)amino)propanoic acid Deposited 2018-06-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	H6J N-{6-[4-(ethenylsulfonyl)-1,4-diazepan-1-yl]-2-(pyridin-2-yl)pyrimidin-4-yl}-beta-alanine × 2 MN MANGANESE (II) ION × 2 GOL GLYCEROL × 2 DMS DIMETHYL SULFOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.59 Å R-free 0.202
6DQ7 LINKED KDM5A JMJ DOMAIN BOUND TO THE POTENTIAL HYDROLYSIS PRODUCT OF INHIBITOR N45 i.e. 3-((6-(4-(2-cyano-3-methylbut-2-enoyl)-1,4-diazepan-1-yl)-2-(pyridin-2-yl)pyrimidin-4-yl)amino)propanoic acid Deposited 2018-06-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	H6M N-{6-[4-(hydroxyacetyl)-1,4-diazepan-1-yl]-2-(pyridin-2-yl)pyrimidin-4-yl}-beta-alanine × 1 MN MANGANESE (II) ION × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.85 Å R-free 0.209
6DQ8 LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N49 i.e. 2-((2-chlorophenyl)(2-(1-methylpyrrolidin-2-yl)ethoxy)methyl)thieno[3,2-b]pyridine-7-carboxylic acid Deposited 2018-06-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	H6S 2-[(R)-(2-chlorophenyl){2-[(2S)-1-methylpyrrolidin-2-yl]ethoxy}methyl]thieno[3,2-b]pyridine-7-carboxylic acid × 1 H6T 2-[(S)-(2-chlorophenyl){2-[(2S)-1-methylpyrrolidin-2-yl]ethoxy}methyl]thieno[3,2-b]pyridine-7-carboxylic acid × 1 MN MANGANESE (II) ION × 1 DMS DIMETHYL SULFOXIDE × 2 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.46 Å R-free 0.210
6DQ9 Linked KDM5A JMJ Domain Bound to the Covalent Inhibitor N69 i.e. [2-((3-acrylamidophenyl)(2-(piperidin-1-yl)ethoxy)methyl)thieno[3,2-b]pyridine-7-carboxylic acid] Deposited 2018-06-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	H74 2-{(R)-[3-(acryloylamino)phenyl][2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid × 1 MN MANGANESE (II) ION × 1 GOL GLYCEROL × 1 DMS DIMETHYL SULFOXIDE × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.75 Å R-free 0.198
6DQA Linked KDM5A JMJ Domain Bound to Inhibitor N70 i.e.[2-((3-aminophenyl)(2-(piperidin-1-yl)ethoxy)methyl)thieno[3,2-b]pyridine-7-carboxylic acid] Deposited 2018-06-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	H6V 2-{(R)-(3-aminophenyl)[2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid × 1 MN MANGANESE (II) ION × 1 GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.89 Å R-free 0.201
6DQB LINKED KDM5A JMJ DOMAIN FORMING COVALENT BOND TO INHIBITOR N71 i.e. 2-((3-(4-(dimethylamino)but-2-enamido)phenyl)(2-(piperidin-1-yl)ethoxy)methyl)thieno[3,2-b]pyridine-7-carboxylic acid Deposited 2018-06-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	H77 2-{(R)-(3-{[(2E)-4-(dimethylamino)but-2-enoyl]amino}phenyl)[2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid × 1 HZV 2-{(R)-(3-{[4-(dimethylamino)butanoyl]amino}phenyl)[2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid × 1 HZM 2-{(S)-(3-{[4-(dimethylamino)butanoyl]amino}phenyl)[2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid × 1 MN MANGANESE (II) ION × 1 GOL GLYCEROL × 2 DMS DIMETHYL SULFOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.79 Å R-free 0.201
6DQC LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N50 i.e. 2-(4-((2-(dimethylamino)ethyl)(ethyl)carbamoyl)-5-(4-methoxyphenyl)-1H-pyrazol-1-yl)isonicotinic acid Deposited 2018-06-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	H5Y 2-[4-{[2-(dimethylamino)ethyl](ethyl)carbamoyl}-5-(4-methoxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic acid × 1 MN MANGANESE (II) ION × 1 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.75 Å R-free 0.215
6DQD LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N53 i.e. 2-(5-([1,1'-biphenyl]-3-yl)-4-(1-(2-(piperidin-1-yl)ethoxy)ethyl)-1H-pyrazol-1-yl)isonicotinic acid Deposited 2018-06-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	H67 2-[5-([1,1'-biphenyl]-3-yl)-4-{(1S)-1-[2-(piperidin-1-yl)ethoxy]ethyl}-1H-pyrazol-1-yl]pyridine-4-carboxylic acid × 1 MN MANGANESE (II) ION × 1 GOL GLYCEROL × 2 DMS DIMETHYL SULFOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.99 Å R-free 0.217
6DQD LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N53 i.e. 2-(5-([1,1'-biphenyl]-3-yl)-4-(1-(2-(piperidin-1-yl)ethoxy)ethyl)-1H-pyrazol-1-yl)isonicotinic acid Deposited 2018-06-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	H67 2-[5-([1,1'-biphenyl]-3-yl)-4-{(1S)-1-[2-(piperidin-1-yl)ethoxy]ethyl}-1H-pyrazol-1-yl]pyridine-4-carboxylic acid × 2 MN MANGANESE (II) ION × 2 GOL GLYCEROL × 4 DMS DIMETHYL SULFOXIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.99 Å R-free 0.217
6DQE LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N67 i.e. 2-(5-phenyl-4-(phenyl(2-(piperidin-1-yl)ethoxy)methyl)-1H-pyrazol-1-yl)isonicotinic acid Deposited 2018-06-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	H6A 2-(5-phenyl-4-{(R)-phenyl[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrazol-1-yl)pyridine-4-carboxylic acid × 1 MN MANGANESE (II) ION × 1 GOL GLYCEROL × 1 DMS DIMETHYL SULFOXIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.69 Å R-free 0.187
6DQE LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N67 i.e. 2-(5-phenyl-4-(phenyl(2-(piperidin-1-yl)ethoxy)methyl)-1H-pyrazol-1-yl)isonicotinic acid Deposited 2018-06-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	H6A 2-(5-phenyl-4-{(R)-phenyl[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrazol-1-yl)pyridine-4-carboxylic acid × 2 MN MANGANESE (II) ION × 2 GOL GLYCEROL × 2 DMS DIMETHYL SULFOXIDE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.69 Å R-free 0.187
6DQF LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N68 i.e. 2-(1-(2-(piperidin-1-yl)ethyl)-1H-benzo[d]imidazol-2-yl)thieno[3,2-b]pyridine-7-carboxylic acid Deposited 2018-06-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Chain A 348–588（241 aa）	Not recorded	H61 2-{1-[2-(piperidin-1-yl)ethyl]-1H-benzimidazol-2-yl}thieno[3,2-b]pyridine-7-carboxylic acid × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate	Resolution 1.69 Å R-free 0.207
7KLO Solution structure of the PHD1 domain of histone demethylase KDM5A Deposited 2020-10-30	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 287–344（58 aa）	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1 NMR sample composition 900 uM U-13C, 99%; U-15N, 99 % PHD1, 50 mM HEPES, 150 mM NaCl, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 550 uM U-13C, 99%; U-15N, 99 % PHD1, 50 mM HEPES, 150 mM NaCl, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
7KLR Solution structure of the PHD1 domain of histone demethylase KDM5A in complex with a histone H3(1-10) peptide Deposited 2020-10-31	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 × 2 PDB declaration: dimeric	Chain A 287–344（58 aa）	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1 NMR sample composition 900 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 4000 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 550 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 800 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1250 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 400 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

45 other PDB entries and 52 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KDM5A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–89； UniProt 1–87 Author chain A； PDBConstruct 90–330； UniProt 348–588

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6bgy
Deposition date deposition_date	2017-10-29
Structure title title	LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(2-(1-methylpyrrolidin-2-yl)ethoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid(Compound 46)
Keywords keywords	DEMETHYLASE INHIBITION, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX, OXIDOREDUCTASE-INHIBITOR complex; OXIDOREDUCTASE/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.10 Å
Radius of gyration Rg (electron density) rg_electron	19.03 Å
Forward intensity I(0) i0	19913100.00
Molecular weight molecular_weight	34405.0 kDa
Excluded volume excluded_volume	43086 Å³
Envelope volume envelope_volume	50313 Å³
Hydration-shell volume shell_volume	21476 Å³
Envelope diameter envelope_diameter	66.8 Å
Shell Rg shell_rg	26.22 Å
Envelope Rg envelope_rg	19.59 Å
Shape Rg shape_rg	19.00 Å
Total Rg total_rg	20.12 Å
Total atoms total_atoms	2424
Residues n_residues	297
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	64.8 Å
Rg (real space) rg_real	20.00 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	1.9910e+07
I(0) uncertainty (real space) i0_real_error	2.1680e+05
Rg (reciprocal space) rg_reciprocal	20.02 Å
I(0) (reciprocal space) i0_reciprocal	19910000.0000
Solution quality estimate total_estimate	0.8128
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.0 Å
Skewness Skewness skewness	0.196
Kurtosis Kurtosis kurtosis	-0.379
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5443000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Lysine-specific demethylase 5A,linked KDM5A JMJ domain
Molecular weight formula_weight	37944.8 kDa
EC 编号 ec_number	1.14.11.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2736

HNMAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRPREAFGFEQAVREYTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-[(S)-(2-chlorophenyl){2-[(2R)-1-methylpyrrolidin-2-yl]ethoxy}methyl]-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid
Molecular weight formula_weight	413.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	263

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6bgyA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

▶

8. Citations (3)

▶

Unit-cell length a length_a	116.685 Å
Unit-cell length b length_b	61.943 Å
Unit-cell length c length_c	46.747 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.22 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.220 Å
Low-resolution limit resolution_low	30.971 Å
R factor r_factor	0.1670
R_work r_work	0.1663
R_free r_free	0.1933

fit	/app/data/saxs_computation/bg/6bgy/6bgy.fit
pddf	/app/data/pr_computation/bg/6bgy/6bgy.pr.out
profile	/app/data/saxs_computation/bg/6bgy/6bgy.dat