2ZL9
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![BU of 2zl9 by Molmil](/molmil-images/mine/2zl9) | 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 analogs: Synthesis, biological evaluation and crystal structure | Descriptor: | (1R,2R,3R,5Z)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethoxy)-9,10-secoestra-5,7,16-triene-1,3-diol, Coactivator peptide DRIP, Vitamin D3 receptor | Authors: | Shimizu, M, Miyamoto, Y, Nakabayashi, M, Masuno, H, Ikura, T, Ito, N. | Deposit date: | 2008-04-04 | Release date: | 2008-06-24 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 analogs: Synthesis, biological evaluation, and crystal structure Bioorg.Med.Chem., 16, 2008
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2ZLC
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![BU of 2zlc by Molmil](/molmil-images/mine/2zlc) | 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 analogs: Synthesis, biological evaluation and crystal structure | 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: | Shimizu, M, Miyamoto, Y, Nakabayashi, M, Masuno, H, Ikura, T, Ito, N. | Deposit date: | 2008-04-04 | Release date: | 2008-06-24 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 analogs: Synthesis, biological evaluation, and crystal structure Bioorg.Med.Chem., 16, 2008
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2ZXN
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![BU of 2zxn by Molmil](/molmil-images/mine/2zxn) | A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket | Descriptor: | (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2S,3S)-3-(2-hydroxyethyl)heptan-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: | Nakabayashi, M, Ikura, T, Ito, N. | Deposit date: | 2009-01-04 | Release date: | 2009-02-17 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | A New Class of Vitamin D Analogues that Induce Structural Rearrangement of the Ligand-Binding Pocket of the Receptor J.Med.Chem., 52, 2009
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7E99
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![BU of 7e99 by Molmil](/molmil-images/mine/7e99) | Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 13% oxygen saturation | Descriptor: | Extracellular giant hemoglobin major globin subunit A1, Extracellular giant hemoglobin major globin subunit A2, Extracellular giant hemoglobin major globin subunit B2, ... | Authors: | Numoto, N, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | Deposit date: | 2021-03-03 | Release date: | 2021-10-06 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state. Iucrj, 8, 2021
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7E97
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![BU of 7e97 by Molmil](/molmil-images/mine/7e97) | Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 58% oxygen saturation | Descriptor: | Extracellular giant hemoglobin major globin subunit A1, Extracellular giant hemoglobin major globin subunit A2, Extracellular giant hemoglobin major globin subunit B2, ... | Authors: | Numoto, N, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | Deposit date: | 2021-03-03 | Release date: | 2021-10-06 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state. Iucrj, 8, 2021
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7E98
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![BU of 7e98 by Molmil](/molmil-images/mine/7e98) | Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 21% oxygen saturation | Descriptor: | Extracellular giant hemoglobin major globin subunit A1, Extracellular giant hemoglobin major globin subunit A2, Extracellular giant hemoglobin major globin subunit B2, ... | Authors: | Numoto, N, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | Deposit date: | 2021-03-03 | Release date: | 2021-10-06 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state. Iucrj, 8, 2021
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7E96
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![BU of 7e96 by Molmil](/molmil-images/mine/7e96) | Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 69% oxygen saturation | Descriptor: | CALCIUM ION, Extracellular giant hemoglobin major globin subunit A1, Extracellular giant hemoglobin major globin subunit A2, ... | Authors: | Numoto, N, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | Deposit date: | 2021-03-03 | Release date: | 2021-10-06 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state. Iucrj, 8, 2021
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7F1I
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![BU of 7f1i by Molmil](/molmil-images/mine/7f1i) | Designed enzyme RA61 M48K/I72D mutant: form II | Descriptor: | Engineered Retroaldolase | Authors: | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | Deposit date: | 2021-06-09 | Release date: | 2021-11-24 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions. Chembiochem, 23, 2022
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7F1H
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![BU of 7f1h by Molmil](/molmil-images/mine/7f1h) | Designed enzyme RA61 M48K/I72D mutant: form I | Descriptor: | Engineered Retroaldolase, FORMIC ACID, GLYCEROL | Authors: | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | Deposit date: | 2021-06-09 | Release date: | 2021-11-24 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.14 Å) | Cite: | Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions. Chembiochem, 23, 2022
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7F1J
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![BU of 7f1j by Molmil](/molmil-images/mine/7f1j) | Designed enzyme RA61 M48K/I72D mutant: form III | Descriptor: | Engineered Retroaldolase | Authors: | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | Deposit date: | 2021-06-09 | Release date: | 2021-11-24 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions. Chembiochem, 23, 2022
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7F1K
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![BU of 7f1k by Molmil](/molmil-images/mine/7f1k) | Designed enzyme RA61 M48K/I72D mutant: form IV | Descriptor: | Engineered Retroaldolase | Authors: | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | Deposit date: | 2021-06-09 | Release date: | 2021-11-24 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.05 Å) | Cite: | Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions. Chembiochem, 23, 2022
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7F1L
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![BU of 7f1l by Molmil](/molmil-images/mine/7f1l) | Designed enzyme RA61 M48K/I72D mutant: form V | Descriptor: | CHLORIDE ION, Engineered Retroaldolase, IMIDAZOLE | Authors: | Fujioka, T, Oka, M, Numoto, N, Ito, N, Oda, M, Tanaka, F. | Deposit date: | 2021-06-09 | Release date: | 2021-11-24 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions. Chembiochem, 23, 2022
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3ANR
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![BU of 3anr by Molmil](/molmil-images/mine/3anr) | human DYRK1A/harmine complex | Descriptor: | 7-METHOXY-1-METHYL-9H-BETA-CARBOLINE, Dual specificity tyrosine-phosphorylation-regulated kinase 1A | Authors: | Nonaka, Y, Hosoya, T, Hagiwara, M, Ito, N. | Deposit date: | 2010-09-06 | Release date: | 2010-11-10 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Development of a novel selective inhibitor of the Down syndrome-related kinase Dyrk1A Nat Commun, 1, 2010
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3ANQ
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![BU of 3anq by Molmil](/molmil-images/mine/3anq) | human DYRK1A/inhibitor complex | Descriptor: | (1Z)-1-(3-ethyl-5-hydroxy-1,3-benzothiazol-2(3H)-ylidene)propan-2-one, Dual specificity tyrosine-phosphorylation-regulated kinase 1A | Authors: | Nonaka, Y, Hosoya, T, Hagiwara, M, Ito, N. | Deposit date: | 2010-09-06 | Release date: | 2010-11-10 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Development of a novel selective inhibitor of the Down syndrome-related kinase Dyrk1A Nat Commun, 1, 2010
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2ZA4
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![BU of 2za4 by Molmil](/molmil-images/mine/2za4) | |
3VRW
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![BU of 3vrw by Molmil](/molmil-images/mine/3vrw) | VDR ligand binding domain in complex with 22S-Butyl-2-methylidene-26,27-dimethyl-19,24-dinor-1alpha,25-dihydroxyvitamin D3 | Descriptor: | (1R,3R,7E,17beta)-17-[(2R,3S)-3-butyl-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | Authors: | Yoshimoto, N, Inaba, Y, Itoh, T, Nakabayashi, M, Ito, N, Yamamoto, K. | Deposit date: | 2012-04-16 | Release date: | 2012-05-23 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands J.Med.Chem., 55, 2012
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3VRV
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![BU of 3vrv by Molmil](/molmil-images/mine/3vrv) | VDR ligand binding domain in complex with 2-Methylidene-26,27-dimethyl-19,24-dinor-1alpha,25-dihydroxyvitamin D3 | Descriptor: | (1R,3R,7E,17beta)-17-[(2R)-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | Authors: | Yoshimoto, N, Inaba, Y, Itoh, T, Nakabayashi, M, Ito, N, Yamamoto, K. | Deposit date: | 2012-04-14 | Release date: | 2012-05-23 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands J.Med.Chem., 55, 2012
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3VJT
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![BU of 3vjt by Molmil](/molmil-images/mine/3vjt) | Vitamin D receptor complex with a carborane compound | Descriptor: | 1-(2-[(R)-2,4-Dihydroxybutoxy]ethyl)-12-(5-ethyl-5-hydroxyheptyl)-1,12-dicarba-closo-dodecaborane, Vitamin D3 receptor, peptide from Mediator of RNA polymerase II transcription subunit 1 | Authors: | Fujii, S, Masuno, M, Kagechika, H, Nakabayashi, M, Ito, N. | Deposit date: | 2011-10-31 | Release date: | 2012-02-08 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Boron Cluster-based Development of Potent Nonsecosteroidal Vitamin D Receptor Ligands: Direct Observation of Hydrophobic Interaction between Protein Surface and Carborane J.Am.Chem.Soc., 133, 2011
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3VJS
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![BU of 3vjs by Molmil](/molmil-images/mine/3vjs) | Vitamin D receptor complex with a carborane compound | Descriptor: | 1-(2-[(S)-2,4-Dihydroxybutoxy]ethyl)-12-(5-ethyl-5-hydroxyheptyl)-1,12-dicarba-closo-dodecaborane, Vitamin D3 receptor, peptide from Mediator of RNA polymerase II transcription subunit 1 | Authors: | Fujii, S, Masuno, M, Kagechika, H, Nakabayashi, M, Ito, N. | Deposit date: | 2011-10-31 | Release date: | 2012-02-08 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.93 Å) | Cite: | Boron Cluster-based Development of Potent Nonsecosteroidal Vitamin D Receptor Ligands: Direct Observation of Hydrophobic Interaction between Protein Surface and Carborane J.Am.Chem.Soc., 133, 2011
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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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2DQU
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![BU of 2dqu by Molmil](/molmil-images/mine/2dqu) | Crystal form II: high resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog | Descriptor: | IMMUNOGLOBULIN 6D9, [1-(3-DIMETHYLAMINO-PROPYL)-3-ETHYL-UREIDO]-[4-(2,2,2-TRIFLUORO-ACETYLAMINO)-BENZYL]PHOSPHINIC ACID-2-(2,2-DIHYDRO-ACETYLAMINO)-3-HYDROXY-1-(4-NITROPHENYL)-PROPYL ESTER | Authors: | Kristensen, O, Vassylyev, D.G, Tanaka, F, Ito, N, Morikawa, K, Fujii, I. | Deposit date: | 2006-05-30 | Release date: | 2006-06-20 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis J.Mol.Biol., 369, 2007
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2DQT
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![BU of 2dqt by Molmil](/molmil-images/mine/2dqt) | High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog | Descriptor: | IMMUNOGLOBULIN 6D9, [1-(3-DIMETHYLAMINO-PROPYL)-3-ETHYL-UREIDO]-[4-(2,2,2-TRIFLUORO-ACETYLAMINO)-BENZYL]PHOSPHINIC ACID-2-(2,2-DIHYDRO-ACETYLAMINO)-3-HYDROXY-1-(4-NITROPHENYL)-PROPYL ESTER | Authors: | Kristensen, O, Vassylyev, D.G, Tanaka, F, Ito, N, Morikawa, K, Fujii, I. | Deposit date: | 2006-05-30 | Release date: | 2006-06-20 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis J.Mol.Biol., 369, 2007
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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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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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