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5ivb

A High Resolution Structure of a Linked KDM5A Jmj Domain with Alpha-Ketoglutarate

Method: X-RAY DIFFRACTION Dmax: 64.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Lysine-specific demethylase 5A,Lysine-specific demethylase 5A

Homo sapiens

UniProt P29375

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 Fragment：Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588,Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588 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

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 5IVB 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 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）
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 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
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 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 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 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 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 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 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 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 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 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）
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 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）
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 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）
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 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）
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
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) Deposited 2017-10-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–87（87 aa）
Chain A 348–588（241 aa）
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
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 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）
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 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）
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 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）
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 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）
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 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）
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 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）
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 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）
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 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）
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 construct 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 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）
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 construct 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 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）
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 construct 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 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）
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 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）
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 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）
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 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）
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 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）
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 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）
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 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）
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 construct 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 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）
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 construct 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 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）
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

SAXS profile for 5ivb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5ivb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5ivb
Deposition date deposition_date2016-03-20
Structure title titleA High Resolution Structure of a Linked KDM5A Jmj Domain with Alpha-Ketoglutarate
Keywords keywordsdemethylase inhibition, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex; OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
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_guinier19.86 Å
Radius of gyration Rg (electron density) rg_electron18.74 Å
Forward intensity I(0) i018967900.00
Molecular weight molecular_weight33344.0 kDa
Excluded volume excluded_volume41695 ų
Envelope volume envelope_volume48047 ų
Hydration-shell volume shell_volume20881 ų
Envelope diameter envelope_diameter65.3 Å
Shell Rg shell_rg25.71 Å
Envelope Rg envelope_rg19.15 Å
Shape Rg shape_rg18.73 Å
Total Rg total_rg19.77 Å
Total atoms total_atoms2353
Residues n_residues293
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 dmax64.7 Å
Rg (real space) rg_real19.74 Å
Rg uncertainty (real space) rg_real_error0.33 Å
I(0) (real space) i0_real1.8970e+07
I(0) uncertainty (real space) i0_real_error2.1610e+05
Rg (reciprocal space) rg_reciprocal19.76 Å
I(0) (reciprocal space) i0_reciprocal18970000.0000
Solution quality estimate total_estimate0.8864
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.6 Å
Skewness Skewness skewness0.191
Kurtosis Kurtosis kurtosis-0.399
Angular range angular_range— – 0.4000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5849000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.996
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id5ivbA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily650 — Cupin
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8. Citations (2)

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9. Files and Curves (10)