Current Protein Identity：P29375
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 2JXJ NMR structure of the ARID domain from the histone H3K4 demethylase RBP2 Deposited 2007-11-20 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 |