1X1U
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1X1Y
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1X1X
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1X1W
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4WUA
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![BU of 4wua by Molmil](/molmil-images/mine/4wua) | Crystal structure of human SRPK1 complexed to an inhibitor SRPIN340 | Descriptor: | CITRIC ACID, N-[2-(1-piperidinyl)-5-(trifluoromethyl)phenyl]-4-pyridinecarboxamide, SRSF protein kinase 1, ... | Authors: | Hoshina, M, Ikura, T, Hosoya, T, Hagiwara, M, Ito, N. | Deposit date: | 2014-10-31 | Release date: | 2015-09-16 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Identification of a Dual Inhibitor of SRPK1 and CK2 That Attenuates Pathological Angiogenesis of Macular Degeneration in Mice Mol.Pharmacol., 88, 2015
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3VTC
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![BU of 3vtc by Molmil](/molmil-images/mine/3vtc) | Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK3 | Descriptor: | (1R,3R,7E,17beta)-17-{(2R,6R)-6-hydroxy-7-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hept-4-yn-2-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, 1,2-ETHANEDIOL, COACTIVATOR PEPTIDE DRIP, ... | Authors: | Nakabayashi, M, Kudo, T, Tokiwa, H, Makishima, M, Yamada, S, Ikura, T, Ito, N. | Deposit date: | 2012-05-26 | Release date: | 2013-06-12 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Combination of Triple Bond and Adamantane Ring on the Vitamin D Side Chain Produced Partial Agonists for Vitamin D Receptor. J.Med.Chem., 2014
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3VTB
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![BU of 3vtb by Molmil](/molmil-images/mine/3vtb) | Crystal structure of rat vitamin D receptor bound to a partial agonist 25-adamantyl-23-yne-19-norvitammin D ADTK1 | Descriptor: | (1R,3R,7E,17beta)-17-{(2R,6S)-6-hydroxy-6-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hex-4-yn-2-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | Authors: | Nakabayashi, M, Kudo, T, Tokiwa, H, Makishima, M, Yamada, S, Ikura, T, Ito, N. | Deposit date: | 2012-05-26 | Release date: | 2013-06-12 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Combination of Triple Bond and Adamantane Ring on the Vitamin D Side Chain Produced Partial Agonists for Vitamin D Receptor. J.Med.Chem., 2014
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5AWJ
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![BU of 5awj by Molmil](/molmil-images/mine/5awj) | Crystal structure of VDR-LBD/partial agonist complex: 22S-hexyl analogue | Descriptor: | (1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,3S)-3-(2-hydroxyethyl)nonan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor,Vitamin D3 receptor | Authors: | Anami, Y, Itoh, T, Inaba, Y, Nakabayashi, M, Ikura, T, Ito, N, Yamamoto, K. | Deposit date: | 2015-07-04 | Release date: | 2015-11-18 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Fine tuning of agonistic/antagonistic activity for vitamin D receptor by 22-alkyl chain length of ligands: 22S-Hexyl compound unexpectedly restored agonistic activity. Bioorg.Med.Chem., 23, 2015
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4YNK
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![BU of 4ynk by Molmil](/molmil-images/mine/4ynk) | Crystal structure of vitamin D receptor ligand binding domain complexed with a 19-norvitamin D compound | Descriptor: | (1R,3R,7E,17beta)-17-{(5S)-5-hydroxy-5-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-1-yl]penta-1,3-diyn-1-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, Coactivator peptide drip from cDNA FLJ50196, highly similar to Peroxisome proliferator-activated receptor-binding protein, ... | Authors: | Watarai, Y, Ikura, T, Ito, N. | Deposit date: | 2015-03-10 | Release date: | 2016-01-20 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Synthesis, Biological Activities, and X-ray Crystal Structural Analysis of 25-Hydroxy-25(or 26)-adamantyl-17-[20(22),23-diynyl]-21-norvitamin D Compounds J.Med.Chem., 58, 2015
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3VT4
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![BU of 3vt4 by Molmil](/molmil-images/mine/3vt4) | Crystal structures of rat VDR-LBD with R270L mutation | Descriptor: | (1R,2Z,3R,5E,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | Deposit date: | 2012-05-19 | Release date: | 2013-05-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands. J.Med.Chem., 56, 2013
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3VT7
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![BU of 3vt7 by Molmil](/molmil-images/mine/3vt7) | Crystal structures of rat VDR-LBD with W282R mutation | Descriptor: | 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | Deposit date: | 2012-05-19 | Release date: | 2013-05-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands. J.Med.Chem., 56, 2013
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3VT6
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![BU of 3vt6 by Molmil](/molmil-images/mine/3vt6) | Crystal structure of rat VDR-LBD with 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 | Descriptor: | (1R,2Z,3R,5E,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | Deposit date: | 2012-05-19 | Release date: | 2013-05-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands. J.Med.Chem., 56, 2013
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3VT5
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![BU of 3vt5 by Molmil](/molmil-images/mine/3vt5) | Crystal structures of rat VDR-LBD with R270L mutation | Descriptor: | (1R,2E,3R,5Z,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | Deposit date: | 2012-05-19 | Release date: | 2013-05-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.11 Å) | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands. J.Med.Chem., 56, 2013
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5AUL
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![BU of 5aul by Molmil](/molmil-images/mine/5aul) | PI3K p85 C-terminal SH2 domain/CD28-derived peptide complex | Descriptor: | GLYCEROL, Phosphatidylinositol 3-kinase regulatory subunit alpha, T-cell-specific surface glycoprotein CD28 | Authors: | Inaba, S, Numoto, N, Morii, H, Ikura, T, Oda, M, Ito, N. | Deposit date: | 2015-04-28 | Release date: | 2016-05-25 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.1 Å) | Cite: | Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins J. Biol. Chem., 292, 2017
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5GJI
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![BU of 5gji by Molmil](/molmil-images/mine/5gji) | PI3K p85 N-terminal SH2 domain/CD28-derived peptide complex | Descriptor: | GLYCEROL, Phosphatidylinositol 3-kinase regulatory subunit alpha, SULFATE ION, ... | Authors: | Inaba, S, Numoto, N, Morii, H, Ogawa, S, Ikura, T, Abe, R, Ito, N, Oda, M. | Deposit date: | 2016-06-30 | Release date: | 2016-12-14 | Last modified: | 2017-05-10 | Method: | X-RAY DIFFRACTION (0.9 Å) | Cite: | Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins J. Biol. Chem., 292, 2017
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5GJH
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![BU of 5gjh by Molmil](/molmil-images/mine/5gjh) | Gads SH2 domain/CD28-derived peptide complex | Descriptor: | GRB2-related adapter protein 2, T-cell-specific surface glycoprotein CD28 | Authors: | Inaba, S, Numoto, N, Morii, H, Ogawa, S, Ikura, T, Abe, R, Ito, N, Oda, M. | Deposit date: | 2016-06-30 | Release date: | 2016-12-14 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.2 Å) | Cite: | Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins J. Biol. Chem., 292, 2017
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7VGP
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7VGO
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![BU of 7vgo by Molmil](/molmil-images/mine/7vgo) | Hen egg lysozyme | Descriptor: | CHLORIDE ION, Lysozyme C, SODIUM ION | Authors: | Oda, M, Ikura, T, Ito, N. | Deposit date: | 2021-09-17 | Release date: | 2022-02-23 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.2 Å) | Cite: | Structural Analysis of Hen Egg Lysozyme Refolded after Denaturation at Acidic pH. Protein J., 41, 2022
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3VTD
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![BU of 3vtd by Molmil](/molmil-images/mine/3vtd) | Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4 | Descriptor: | (1R,3R,7E,17beta)-17-{(2R,6S)-6-hydroxy-7-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hept-4-yn-2-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | Authors: | Nakabayashi, M, Kudo, T, Tokiwa, H, Makishima, M, Yamada, S, Ikura, T, Ito, N. | Deposit date: | 2012-05-26 | Release date: | 2013-06-12 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Combination of Triple Bond and Adamantane Ring on the Vitamin D Side Chain Produced Partial Agonists for Vitamin D Receptor. J.Med.Chem., 2014
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5XZF
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![BU of 5xzf by Molmil](/molmil-images/mine/5xzf) | Vitamin D receptor with a synthetic ligand ADRO1 | Descriptor: | (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,6S)-6-(1-adamantyl)-6-oxidanyl-hex-4-yn-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol, FORMIC ACID, Mediator of RNA polymerase II transcription subunit 1, ... | Authors: | Otero, R, Numoto, N, Ikura, T, Yamada, S, Mourino, A, Makishima, M, Ito, N. | Deposit date: | 2017-07-12 | Release date: | 2018-07-25 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | 25 S-Adamantyl-23-yne-26,27-dinor-1 alpha ,25-dihydroxyvitamin D3: Synthesis, Tissue Selective Biological Activities, and X-ray Crystal Structural Analysis of Its Vitamin D Receptor Complex. J. Med. Chem., 61, 2018
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5XZH
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![BU of 5xzh by Molmil](/molmil-images/mine/5xzh) | Vitamin D receptor with a synthetic ligand ADRO2 | Descriptor: | (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,6R)-6-(1-adamantyl)-6-oxidanyl-hex-4-yn-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | Authors: | Otero, R, Numoto, N, Ikura, T, Yamada, S, Mourino, A, Makishima, M, Ito, N. | Deposit date: | 2017-07-12 | Release date: | 2018-07-25 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | 25 S-Adamantyl-23-yne-26,27-dinor-1 alpha ,25-dihydroxyvitamin D3: Synthesis, Tissue Selective Biological Activities, and X-ray Crystal Structural Analysis of Its Vitamin D Receptor Complex. J. Med. Chem., 61, 2018
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3WTQ
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![BU of 3wtq by Molmil](/molmil-images/mine/3wtq) | Crystal structure of VDR-LBD complexed with 22S-butyl-2-methylidene-19-nor-1a,25-dihydroxyvitamin D3 | Descriptor: | (1R,3R,7E,17beta)-17-[(2R,3S)-3-butyl-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | Authors: | Nakabayashi, M, Inaba, Y, Itoh, T, Anami, Y, Ikura, T, Ito, N, Yamamoto, K. | Deposit date: | 2014-04-15 | Release date: | 2015-04-15 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Crystal structure of VDR-LBD complexed with 22S-butyl-2-methylidene-19-nor-1a,25-dihydroxyvitamin D3 To be Published
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5ZQU
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![BU of 5zqu by Molmil](/molmil-images/mine/5zqu) | Crystal structure of tetrameric RXRalpha-LBD complexed with partial agonist CBt-PMN | Descriptor: | 1-(3,5,5,8,8-pentamethyl-6,7-dihydronaphthalen-2-yl)benzotriazole-5-carboxylic acid, BROMIDE ION, Retinoic acid receptor RXR-alpha | Authors: | Miyashita, Y, Numoto, N, Arulmozhiraja, S, Nakano, S, Matsuo, N, Shimizu, K, Kakuta, H, Ito, S, Ikura, T, Ito, N, Tokiwa, H. | Deposit date: | 2018-04-20 | Release date: | 2019-02-27 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.60038781 Å) | Cite: | Dual conformation of the ligand induces the partial agonistic activity of retinoid X receptor alpha (RXR alpha ). FEBS Lett., 593, 2019
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3VT3
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![BU of 3vt3 by Molmil](/molmil-images/mine/3vt3) | Crystal structures of rat VDR-LBD with R270L mutation | Descriptor: | 1,2-ETHANEDIOL, 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL, COACTIVATOR PEPTIDE DRIP, ... | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | Deposit date: | 2012-05-19 | Release date: | 2013-05-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands. J.Med.Chem., 56, 2013
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3VT9
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![BU of 3vt9 by Molmil](/molmil-images/mine/3vt9) | Crystal structures of rat VDR-LBD with W282R mutation | Descriptor: | (1R,2Z,3R,5E,7E,9beta,17beta)-2-(2-hydroxyethylidene)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9-(prop-2-en-1-yl)-9,10-secoestra-5,7-diene-1,3-diol, COACTIVATOR PEPTIDE DRIP, Vitamin D3 receptor | Authors: | Nakabayashi, M, Shimizu, M, Ikura, T, Ito, N. | Deposit date: | 2012-05-19 | Release date: | 2013-05-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands. J.Med.Chem., 56, 2013
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