5VAR
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5TVS
| JMJD2A in complex with Ni(II) | Descriptor: | Lysine-specific demethylase 4A, NICKEL (II) ION, ZINC ION | Authors: | Cascella, B, Lee, S.G, Jez, J.M. | Deposit date: | 2016-11-09 | Release date: | 2017-02-01 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.745 Å) | Cite: | The small molecule JIB-04 disrupts O2 binding in the Fe-dependent histone demethylase KDM4A/JMJD2A. Chem. Commun. (Camb.), 53, 2017
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5TVR
| JMJD2A in complex with Ni(II) and alpha-Ketoglutarate | Descriptor: | 2-OXOGLUTARIC ACID, Lysine-specific demethylase 4A, NICKEL (II) ION, ... | Authors: | Cascella, B, Lee, S.G, Jez, J.M. | Deposit date: | 2016-11-09 | Release date: | 2017-02-01 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.093 Å) | Cite: | The small molecule JIB-04 disrupts O2 binding in the Fe-dependent histone demethylase KDM4A/JMJD2A. Chem. Commun. (Camb.), 53, 2017
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5LY1
| JMJD2A/ KDM4A COMPLEXED WITH NI(II) AND Macrocyclic PEPTIDE Inhibitor CP2 (13-mer) | Descriptor: | CHLORIDE ION, CP2, GLYCEROL, ... | Authors: | King, O.N.F, Chowdhury, R, Kawamura, A, Schofield, C.J. | Deposit date: | 2016-09-23 | Release date: | 2017-04-12 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Highly selective inhibition of histone demethylases by de novo macrocyclic peptides. Nat Commun, 8, 2017
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5LY2
| JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Macrocyclic PEPTIDE Inhibitor CP2_R6Kme3 (13-mer) | Descriptor: | CHLORIDE ION, CP2_R6Kme3, GLYCEROL, ... | Authors: | Chowdhury, R, Madden, S.K, Hopkinson, R, Schofield, C.J. | Deposit date: | 2016-09-23 | Release date: | 2017-04-12 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.43 Å) | Cite: | Highly selective inhibition of histone demethylases by de novo macrocyclic peptides. Nat Commun, 8, 2017
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5D6X
| Crystal structure of double tudor domain of human lysine demethylase KDM4A | Descriptor: | Lysine-specific demethylase 4A, SULFATE ION | Authors: | Wang, F, Su, Z, Denu, J.M, Phillips Jr, G.N, Enzyme Discovery for Natural Product Biosynthesis (NatPro) | Deposit date: | 2015-08-13 | Release date: | 2015-11-25 | Last modified: | 2024-03-06 | Method: | X-RAY DIFFRACTION (2.153 Å) | Cite: | Reader domain specificity and lysine demethylase-4 family function. Nat Commun, 7, 2016
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5D6Y
| Crystal structure of double tudor domain of human lysine demethylase KDM4A complexed with histone H3K23me3 | Descriptor: | Lysine-specific demethylase 4A, peptide H3K23me3 (19-28) | Authors: | Wang, F, Su, Z, Miller, M.D, Denu, J.M, Phillips Jr, G.N, Enzyme Discovery for Natural Product Biosynthesis (NatPro) | Deposit date: | 2015-08-13 | Release date: | 2016-02-10 | Last modified: | 2019-12-25 | Method: | X-RAY DIFFRACTION (2.287 Å) | Cite: | Reader domain specificity and lysine demethylase-4 family function. Nat Commun, 7, 2016
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5D6W
| Crystal structure of double tudor domain of human lysine demethylase KDM4A | Descriptor: | Lysine-specific demethylase 4A, S,R MESO-TARTARIC ACID | Authors: | Wang, F, Su, Z, Denu, J.M, Phillips Jr, G.N, Enzyme Discovery for Natural Product Biosynthesis (NatPro) | Deposit date: | 2015-08-13 | Release date: | 2015-11-25 | Last modified: | 2024-03-06 | Method: | X-RAY DIFFRACTION (1.992 Å) | Cite: | Reader domain specificity and lysine demethylase-4 family function. Nat Commun, 7, 2016
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6H4P
| Crystal structure of human KDM4A in complex with compound 16a | Descriptor: | 8-[4-[2-[4-(3-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one, CHLORIDE ION, DIMETHYL SULFOXIDE, ... | Authors: | Le Bihan, Y.V, van Montfort, R.L.M. | Deposit date: | 2018-07-23 | Release date: | 2019-06-12 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.19 Å) | Cite: | C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur.J.Med.Chem., 177, 2019
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6H4Y
| Crystal structure of human KDM4A in complex with compound 17e | Descriptor: | 8-[4-[2-[4-[4-(2-morpholin-4-ylethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one, CHLORIDE ION, DIMETHYL SULFOXIDE, ... | Authors: | Le Bihan, Y.V, van Montfort, R.L.M. | Deposit date: | 2018-07-23 | Release date: | 2019-06-12 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.38 Å) | Cite: | C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur.J.Med.Chem., 177, 2019
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6H4W
| Crystal structure of human KDM4A in complex with compound 19d | Descriptor: | 8-[4-[2-[4-(3-chlorophenyl)-4-methyl-piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one, CHLORIDE ION, DIMETHYL SULFOXIDE, ... | Authors: | Le Bihan, Y.V, van Montfort, R.L.M. | Deposit date: | 2018-07-23 | Release date: | 2019-06-12 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.81 Å) | Cite: | C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur.J.Med.Chem., 177, 2019
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6H4U
| Crystal structure of human KDM4A in complex with compound 34b | Descriptor: | 8-[4-(1-methylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one, CHLORIDE ION, DIMETHYL SULFOXIDE, ... | Authors: | Le Bihan, Y.V, van Montfort, R.L.M. | Deposit date: | 2018-07-23 | Release date: | 2019-06-12 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.21 Å) | Cite: | C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur.J.Med.Chem., 177, 2019
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6H4X
| Crystal structure of human KDM4A in complex with compound 17b | Descriptor: | 8-[4-[2-[4-(4-pyridin-3-ylphenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one, CHLORIDE ION, DIMETHYL SULFOXIDE, ... | Authors: | Le Bihan, Y.V, van Montfort, R.L.M. | Deposit date: | 2018-07-23 | Release date: | 2019-06-12 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.34 Å) | Cite: | C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur.J.Med.Chem., 177, 2019
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6H4S
| Crystal structure of human KDM4A in complex with compound 16m | Descriptor: | 8-[4-[2-[4-[3-[2-(dimethylamino)ethyl]phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one, CHLORIDE ION, DIMETHYL SULFOXIDE, ... | Authors: | Le Bihan, Y.V, van Montfort, R.L.M. | Deposit date: | 2018-07-23 | Release date: | 2019-06-12 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.45 Å) | Cite: | C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur.J.Med.Chem., 177, 2019
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6H4Q
| Crystal structure of human KDM4A in complex with compound 34a | Descriptor: | 8-[4-(1-methylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one, CHLORIDE ION, DIMETHYL SULFOXIDE, ... | Authors: | Le Bihan, Y.V, van Montfort, R.L.M. | Deposit date: | 2018-07-23 | Release date: | 2019-06-12 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.31 Å) | Cite: | C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur.J.Med.Chem., 177, 2019
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6H4T
| Crystal structure of human KDM4A in complex with compound 19a | Descriptor: | 8-[4-(2-spiro[1,2-dihydroindene-3,4'-piperidine]-1'-ylethyl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one, CHLORIDE ION, DIMETHYL SULFOXIDE, ... | Authors: | Le Bihan, Y.V, van Montfort, R.L.M. | Deposit date: | 2018-07-23 | Release date: | 2019-06-12 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.38 Å) | Cite: | C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur.J.Med.Chem., 177, 2019
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6H4V
| Crystal structure of human KDM4A in complex with compound 34g | Descriptor: | 8-[4-(1-cyclopentylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one, CHLORIDE ION, DIMETHYL SULFOXIDE, ... | Authors: | Le Bihan, Y.V, van Montfort, R.L.M. | Deposit date: | 2018-07-23 | Release date: | 2019-06-12 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.15 Å) | Cite: | C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur.J.Med.Chem., 177, 2019
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6H4R
| Crystal structure of human KDM4A in complex with compound 17f | Descriptor: | 8-[4-[2-[4-[4-[2-(dimethylamino)ethyl]phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one, CHLORIDE ION, DIMETHYL SULFOXIDE, ... | Authors: | Le Bihan, Y.V, van Montfort, R.L.M. | Deposit date: | 2018-07-23 | Release date: | 2019-06-12 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.14 Å) | Cite: | C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur.J.Med.Chem., 177, 2019
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6H4O
| Crystal structure of human KDM4A in complex with compound 18a | Descriptor: | 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one, CHLORIDE ION, DIMETHYL SULFOXIDE, ... | Authors: | Le Bihan, Y.V, van Montfort, R.L.M. | Deposit date: | 2018-07-23 | Release date: | 2019-06-12 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur.J.Med.Chem., 177, 2019
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6H8P
| JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K26me3 peptide (15-mer) | Descriptor: | CHLORIDE ION, GLYCEROL, Histone H1.4, ... | Authors: | Chowdhury, R, Walport, L.J, Schofield, C.J. | Deposit date: | 2018-08-03 | Release date: | 2018-08-15 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.983 Å) | Cite: | Mechanistic and structural studies of KDM-catalysed demethylation of histone 1 isotype 4 at lysine 26. FEBS Lett., 592, 2018
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7EQV
| Crystal structure of JMJD2A complexed with 3,4-dihydroxybenzoic acid | Descriptor: | 3,4-DIHYDROXYBENZOIC ACID, CHLORIDE ION, Lysine-specific demethylase 4A, ... | Authors: | Fang, W.-K, Yang, S.-M, Wang, W.-C. | Deposit date: | 2021-05-04 | Release date: | 2022-05-18 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Natural product myricetin is a pan-KDM4 inhibitor which with poly lactic-co-glycolic acid formulation effectively targets castration-resistant prostate cancer. J.Biomed.Sci., 29, 2022
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6CG1
| Crystal Structure of KDM4A with Compound 14 | Descriptor: | 3-{[(4-fluorophenyl)methyl]amino}pyridine-4-carboxylic acid, Lysine-specific demethylase 4A, NICKEL (II) ION, ... | Authors: | Hosfield, D.J, Nie, Z. | Deposit date: | 2018-02-19 | Release date: | 2018-04-18 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.16 Å) | Cite: | Structure-based design and discovery of potent and selective KDM5 inhibitors. Bioorg. Med. Chem. Lett., 28, 2018
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6CG2
| Crystal Structure of KDM4A with Compound 8 | Descriptor: | 2-[5-(3-hydroxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic acid, Lysine-specific demethylase 4A, NICKEL (II) ION, ... | Authors: | Hosfield, D.J, Nie, Z. | Deposit date: | 2018-02-19 | Release date: | 2018-04-18 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.34 Å) | Cite: | Structure-based design and discovery of potent and selective KDM5 inhibitors. Bioorg. Med. Chem. Lett., 28, 2018
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5F2W
| Crystal structure of human KDM4A in complex with compound 16 | Descriptor: | 1,2-ETHANEDIOL, 2-(2-azanyl-1,3-thiazol-4-yl)pyridine-4-carboxamide, DIMETHYL SULFOXIDE, ... | Authors: | Le Bihan, Y.-V, Dempster, S, Westwood, I.M, van Montfort, R.L.M. | Deposit date: | 2015-12-02 | Release date: | 2016-01-20 | Last modified: | 2024-01-10 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors. J.Med.Chem., 59, 2016
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5A7O
| Crystal structure of human JMJD2A in complex with compound 42 | Descriptor: | 1,2-ETHANEDIOL, 2-[5-(2-methoxyethanoylamino)-2-oxidanyl-phenyl]pyridine-4-carboxylic acid, DIMETHYL SULFOXIDE, ... | Authors: | Nowak, R, Velupillai, S, Krojer, T, Gileadi, C, Johansson, C, Korczynska, M, Le, D.D, Younger, N, Gregori-Puigjane, E, Tumber, A, Iwasa, E, Pollock, S.B, Ortiz Torres, I, Pinkas, D.M, von Delft, F, Arrowsmith, C.H, Bountra, C, Edwards, A, Shoichet, B.K, Fujimori, D.G, Oppermann, U. | Deposit date: | 2015-07-09 | Release date: | 2016-01-13 | Last modified: | 2024-01-10 | Method: | X-RAY DIFFRACTION (2.15 Å) | Cite: | Docking and Linking of Fragments to Discover Jumonji Histone Demethylase Inhibitors. J.Med.Chem., 59, 2016
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