5AV9
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![BU of 5av9 by Molmil](/molmil-images/mine/5av9) | human nucleosome core particle | Descriptor: | DNA (147-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Wakamori, M, Fujii, Y, Umehara, T, Yokoyama, S. | Deposit date: | 2015-06-12 | Release date: | 2015-12-23 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation Sci Rep, 5, 2015
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5AV8
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![BU of 5av8 by Molmil](/molmil-images/mine/5av8) | human nucleosome core particle | Descriptor: | DNA (147-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Wakamori, M, Fujii, Y, Umehara, T, Yokoyama, S. | Deposit date: | 2015-06-12 | Release date: | 2015-12-23 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation Sci Rep, 5, 2015
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5AV6
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![BU of 5av6 by Molmil](/molmil-images/mine/5av6) | human nucleosome core particle | Descriptor: | DNA (147-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Wakamori, M, Fujii, Y, Umehara, T, Yokoyama, S. | Deposit date: | 2015-06-12 | Release date: | 2015-12-23 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation Sci Rep, 5, 2015
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7EIC
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![BU of 7eic by Molmil](/molmil-images/mine/7eic) | |
7EID
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![BU of 7eid by Molmil](/molmil-images/mine/7eid) | |
7EIE
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![BU of 7eie by Molmil](/molmil-images/mine/7eie) | Crystal structure of YEATS2 YEATS domain | Descriptor: | GLYCEROL, YEATS domain-containing protein 2 | Authors: | Kikuchi, M, Umehara, T. | Deposit date: | 2021-03-30 | Release date: | 2022-04-06 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.67 Å) | Cite: | Elucidation of binding preferences of YEATS domains to site-specific acetylated nucleosome core particles. J.Biol.Chem., 298, 2022
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5B2J
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![BU of 5b2j by Molmil](/molmil-images/mine/5b2j) | Human nucleosome containing CpG methylated DNA | Descriptor: | DNA (146-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Fujii, Y, Wakamori, M, Umehara, T, Yokoyama, S. | Deposit date: | 2016-01-18 | Release date: | 2016-06-15 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Crystal structure of human nucleosome core particle containing enzymatically introduced CpG methylation. Febs Open Bio, 6, 2016
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5AV5
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![BU of 5av5 by Molmil](/molmil-images/mine/5av5) | human nucleosome core particle | Descriptor: | DNA (147-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Wakamori, M, Fujii, Y, Umehara, T, Yokoyama, S. | Deposit date: | 2015-06-11 | Release date: | 2015-12-23 | Last modified: | 2020-02-19 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation Sci Rep, 5, 2015
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5AVC
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![BU of 5avc by Molmil](/molmil-images/mine/5avc) | human nucleosome core particle | Descriptor: | DNA (147-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Wakamori, M, Fujii, Y, Umehara, T, Yokoyama, S. | Deposit date: | 2015-06-12 | Release date: | 2015-12-23 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation Sci Rep, 5, 2015
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3ABU
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![BU of 3abu by Molmil](/molmil-images/mine/3abu) | Crystal Structure of LSD1 in complex with a 2-PCPA derivative, S1201 | Descriptor: | Lysine-specific histone demethylase 1, [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(1R,3R,3aS)-3-[2-(benzyloxy)-3-fluorophenyl]-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate | Authors: | Mimasu, S, Umezawa, N, Sato, S, Higuchi, T, Umehara, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2009-12-21 | Release date: | 2010-07-07 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (3.1 Å) | Cite: | Structurally Designed trans-2-Phenylcyclopropylamine Derivatives Potently Inhibit Histone Demethylase LSD1/KDM1 Biochemistry, 49, 2010
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3ABT
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![BU of 3abt by Molmil](/molmil-images/mine/3abt) | Crystal Structure of LSD1 in complex with trans-2-pentafluorophenylcyclopropylamine | Descriptor: | Lysine-specific histone demethylase 1, [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(1R,3R,3aS)-1-hydroxy-10,11-dimethyl-4,6-dioxo-3-(pentafluorophenyl)-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate | Authors: | Mimasu, S, Umezawa, N, Sato, S, Higuchi, T, Umehara, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2009-12-21 | Release date: | 2010-07-07 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Structurally Designed trans-2-Phenylcyclopropylamine Derivatives Potently Inhibit Histone Demethylase LSD1/KDM1 Biochemistry, 49, 2010
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2Z3Y
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![BU of 2z3y by Molmil](/molmil-images/mine/2z3y) | Crystal structure of Lysine-specific demethylase1 | Descriptor: | Lysine-specific histone demethylase 1, [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4S)-5-[7,8-DIMETHYL-2,4-DIOXO-5-(3-PHENYLPROPANOYL)-1,3,4,5-TETRAHYDROBENZO[G]PTERIDIN-10(2H)-YL]-2,3,4-TRIHYDROXYPENTYL DIHYDROGEN DIPHOSPHATE | Authors: | Mimasu, S, Sengoku, T, Umehara, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-06-08 | Release date: | 2008-01-01 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25A Biochem.Biophys.Res.Commun., 366, 2008
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5B2I
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![BU of 5b2i by Molmil](/molmil-images/mine/5b2i) | Human nucleosome containing CpG unmethylated DNA | Descriptor: | DNA (146-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Fujii, Y, Wakamori, M, Umehara, T, Yokoyama, S. | Deposit date: | 2016-01-16 | Release date: | 2016-06-15 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Crystal structure of human nucleosome core particle containing enzymatically introduced CpG methylation. Febs Open Bio, 6, 2016
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5ZQQ
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![BU of 5zqq by Molmil](/molmil-images/mine/5zqq) | Tankyrase-2 in complex with compound 52 | Descriptor: | 1-methyl-1'-(4-oxo-3,4,5,6,7,8-hexahydroquinazolin-2-yl)spiro[indole-3,4'-piperidin]-2(1H)-one, GLYCEROL, PHOSPHATE ION, ... | Authors: | Niwa, H, Shirai, F, Sato, S, Yoshimoto, N, Tsumura, T, Okue, M, Shirouzu, M, Seimiya, H, Umehara, T. | Deposit date: | 2018-04-19 | Release date: | 2019-04-03 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.29 Å) | Cite: | Discovery of Novel Spiroindoline Derivatives as Selective Tankyrase Inhibitors. J. Med. Chem., 62, 2019
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5ZQO
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![BU of 5zqo by Molmil](/molmil-images/mine/5zqo) | Tankyrase-2 in complex with compound 1a | Descriptor: | 2-[4-(2-methoxyphenyl)piperazin-1-yl]-5,6,7,8-tetrahydroquinazolin-4(3H)-one, GLYCEROL, SULFATE ION, ... | Authors: | Niwa, H, Shirai, F, Sato, S, Yoshimoto, N, Tsumura, T, Okue, M, Shirouzu, M, Seimiya, H, Umehara, T. | Deposit date: | 2018-04-19 | Release date: | 2019-04-03 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.06 Å) | Cite: | Discovery of Novel Spiroindoline Derivatives as Selective Tankyrase Inhibitors. J. Med. Chem., 62, 2019
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5ZQP
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![BU of 5zqp by Molmil](/molmil-images/mine/5zqp) | Tankyrase-2 in complex with compound 12 | Descriptor: | 1'-(4-oxo-3,4,5,6,7,8-hexahydroquinazolin-2-yl)-2H-spiro[1-benzofuran-3,4'-piperidin]-2-one, GLYCEROL, PHOSPHATE ION, ... | Authors: | Niwa, H, Shirai, F, Sato, S, Yoshimoto, N, Tsumura, T, Okue, M, Shirouzu, M, Seimiya, H, Umehara, T. | Deposit date: | 2018-04-19 | Release date: | 2019-04-03 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.99 Å) | Cite: | Discovery of Novel Spiroindoline Derivatives as Selective Tankyrase Inhibitors. J. Med. Chem., 62, 2019
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5ZQR
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![BU of 5zqr by Molmil](/molmil-images/mine/5zqr) | Tankyrase-2 in complex with compound 40c | Descriptor: | 2-[4,6-difluoro-1-(2-hydroxyethyl)-1,2-dihydro-1'H-spiro[indole-3,4'-piperidin]-1'-yl]-5,6,7,8-tetrahydroquinazolin-4(3H)-one, GLYCEROL, PHOSPHATE ION, ... | Authors: | Niwa, H, Shirai, F, Sato, S, Yoshimoto, N, Tsumura, T, Okue, M, Shirouzu, M, Seimiya, H, Umehara, T. | Deposit date: | 2018-04-19 | Release date: | 2019-04-03 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Discovery of Novel Spiroindoline Derivatives as Selective Tankyrase Inhibitors. J. Med. Chem., 62, 2019
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6A84
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![BU of 6a84 by Molmil](/molmil-images/mine/6a84) | Tankyrase-2 in complex with compound 15d | Descriptor: | 2-(4-chloro-1,2-dihydro-1'H-spiro[indole-3,4'-piperidin]-1'-yl)-5,6,7,8-tetrahydroquinazolin-4(3H)-one, GLYCEROL, PHOSPHATE ION, ... | Authors: | Niwa, H, Shirai, F, Sato, S, Yoshimoto, N, Tsumura, T, Okue, M, Shirouzu, M, Seimiya, H, Umehara, T. | Deposit date: | 2018-07-06 | Release date: | 2019-04-03 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.98 Å) | Cite: | Discovery of Novel Spiroindoline Derivatives as Selective Tankyrase Inhibitors. J. Med. Chem., 62, 2019
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3ABH
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![BU of 3abh by Molmil](/molmil-images/mine/3abh) | Crystal structure of the EFC/F-BAR domain of human PACSIN2/Syndapin II (2.0 A) | Descriptor: | Protein kinase C and casein kinase substrate in neurons protein 2 | Authors: | Shimada, A, Shirouzu, M, Hanawa-Suetsugu, K, Terada, T, Umehara, T, Suetsugu, S, Yamamoto, M, Yokoyama, S. | Deposit date: | 2009-12-11 | Release date: | 2010-04-14 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Mapping of the basic amino-acid residues responsible for tubulation and cellular protrusion by the EFC/F-BAR domain of pacsin2/Syndapin II Febs Lett., 584, 2010
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3ACO
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![BU of 3aco by Molmil](/molmil-images/mine/3aco) | Crystal structure of the EFC/F-BAR domain of human PACSIN2/Syndapin II (2.7 A) | Descriptor: | CALCIUM ION, Protein kinase C and casein kinase substrate in neurons protein 2 | Authors: | Shimada, A, Shirouzu, M, Hanawa-Suetsugu, K, Terada, T, Umehara, T, Suetsugu, S, Yamamoto, M, Yokoyama, S. | Deposit date: | 2010-01-07 | Release date: | 2010-04-14 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Mapping of the basic amino-acid residues responsible for tubulation and cellular protrusion by the EFC/F-BAR domain of pacsin2/Syndapin II Febs Lett., 584, 2010
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5YE4
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![BU of 5ye4 by Molmil](/molmil-images/mine/5ye4) | Crystal structure of the complex of di-acetylated histone H4 and 1A9D7 Fab fragment | Descriptor: | 1A9D7 L chain, 1A9D7 VH CH1 chain, ZINC ION, ... | Authors: | Matsuda, T, Ito, T, Wakamori, M, Umehara, T. | Deposit date: | 2017-09-15 | Release date: | 2018-08-22 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.799 Å) | Cite: | JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states. Epigenetics, 13, 2018
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5YLT
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![BU of 5ylt by Molmil](/molmil-images/mine/5ylt) | Crystal structure of SET7/9 in complex with a cyproheptadine derivative | Descriptor: | 2-(1-methylpiperidin-4-ylidene)tricyclo[9.4.0.0^{3,8}]pentadeca-1(11),3(8),4,6,9,12,14-heptaen-6-ol, GLYCEROL, Histone-lysine N-methyltransferase SETD7, ... | Authors: | Hirano, T, Fujiwara, T, Niwa, H, Hirano, M, Ohira, K, Okazaki, Y, Sato, S, Umehara, T, Maemoto, Y, Ito, A, Yoshida, M, Kagechika, H. | Deposit date: | 2017-10-19 | Release date: | 2018-06-20 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.69 Å) | Cite: | Development of Novel Inhibitors for Histone Methyltransferase SET7/9 based on Cyproheptadine. ChemMedChem, 13, 2018
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5YE3
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![BU of 5ye3 by Molmil](/molmil-images/mine/5ye3) | Crystal structure of the complex of di-acetylated histone H4 and 2A7D9 Fab fragment | Descriptor: | 2A7D9 L chain, 2A7D9 VH CH1 chain, di-acetylated histone H4 | Authors: | Matsuda, T, Ito, T, Wakamori, M, Umehara, T. | Deposit date: | 2017-09-15 | Release date: | 2018-08-22 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states. Epigenetics, 13, 2018
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5X60
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![BU of 5x60 by Molmil](/molmil-images/mine/5x60) | Crystal structure of LSD1-CoREST in complex with peptide 9 | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, Lysine-specific histone demethylase 1A, ... | Authors: | Kikuchi, M, Amano, Y, Sato, S, Yokoyama, S, Umezawa, N, Higuchi, T, Umehara, T. | Deposit date: | 2017-02-20 | Release date: | 2017-04-12 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.69 Å) | Cite: | Development and crystallographic evaluation of histone H3 peptide with N-terminal serine substitution as a potent inhibitor of lysine-specific demethylase 1. Bioorg. Med. Chem., 25, 2017
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5YJB
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![BU of 5yjb by Molmil](/molmil-images/mine/5yjb) | LSD1-CoREST in complex with 4-[5-(piperidin-4-ylmethoxy)-2-(p-tolyl)pyridin-3-yl]benzonitrile | Descriptor: | 4-[2-(4-methylphenyl)-5-(piperidin-4-ylmethoxy)pyridin-3-yl]benzenecarbonitrile, FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, ... | Authors: | Niwa, H, Sato, S, Hashimoto, T, Matsuno, K, Umehara, T. | Deposit date: | 2017-10-10 | Release date: | 2018-07-04 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.96 Å) | Cite: | Crystal Structure of LSD1 in Complex with 4-[5-(Piperidin-4-ylmethoxy)-2-(p-tolyl)pyridin-3-yl]benzonitrile. Molecules, 23, 2018
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