3W1F
 
 | | Crystal structure of Human MPS1 catalytic domain in complex with 5-(5-ethoxy-6-(1-methyl-1H-pyrazol-4-yl)-1H-indazol-3-yl)-2-methylbenzenesulfonamide | | Descriptor: | 5-[5-ethoxy-6-(1-methyl-1H-pyrazol-4-yl)-1H-indazol-3-yl]-2-methylbenzenesulfonamide, Dual specificity protein kinase TTK | | Authors: | Kusakabe, K, Ide, N, Daigo, Y, Tachibana, Y, Itoh, T, Yamamoto, T, Hashizume, H, Hato, Y, Higashino, K, Okano, Y, Sato, Y, Inoue, M, Iguchi, M, Kanazawa, T, Ishioka, Y, Dohi, K, Kido, Y, Sakamoto, S, Yasuo, K, Maeda, M, Higaki, M, Ueda, K, Yoshizawa, H, Baba, Y, Shiota, T, Murai, H, Nakamura, Y. | | Deposit date: | 2012-11-14 | | Release date: | 2013-06-26 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Indazole-based potent and cell-active Mps1 kinase inhibitors: rational design from pan-kinase inhibitor anthrapyrazolone (SP600125)
J.Med.Chem., 56, 2013
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3A74
 | | Lysyl-tRNA synthetase from Bacillus stearothermophilus complexed with Diadenosine Tetraphosphate (AP4A) | | Descriptor: | 2,6-DIAMINO-HEXANOIC ACID AMIDE, BIS(ADENOSINE)-5'-TETRAPHOSPHATE, Lysyl-tRNA synthetase, ... | | Authors: | Sakurama, H, Takita, T, Mikami, B, Itoh, T, Yasukawa, K, Inouye, K. | | Deposit date: | 2009-09-13 | | Release date: | 2010-09-22 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal Structure of Lysyl-tRNA Synthetase from Bacillus stearothermophilus in Complex with Diadenosine Tetraphosphate (AP4A): Insights into AP4A Synthesis Mechanisms and Implication for Recognition of Discriminator Base of tRNA^Lys
To be Published
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3W6X
 | | Yeast N-acetyltransferase Mpr1 in complex with CHOP | | Descriptor: | (4S)-4-hydroxy-L-proline, CHLORIDE ION, HEXAETHYLENE GLYCOL, ... | | Authors: | Nasuno, R, Hirano, Y, Itoh, T, Hakoshima, T, Hibi, T, Takagi, H. | | Deposit date: | 2013-02-25 | | Release date: | 2013-08-07 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (2.299 Å) | | Cite: | Structural and functional analysis of the yeast N-acetyltransferase Mpr1 involved in oxidative stress tolerance via proline metabolism
Proc.Natl.Acad.Sci.USA, 110, 2013
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3AFR
 | | Crystal Structure of VDR-LBD/22S-Butyl-1a,24R-dihydroxyvitamin D3 complex | | Descriptor: | (1R,3S,5Z)-5-[(2E)-2-{(1R,3aS,7aR)-1-[(1R,2S,4R)-2-butyl-4-hydroxy-1,5-dimethylhexyl]-7a-methyloctahydro-4H-inden-4-yli dene}ethylidene]-4-methylidenecyclohexane-1,3-diol, 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Inaba, Y, Nakabayashi, M, Itoh, T, Ikura, T, Ito, N, Yamamoto, K. | | Deposit date: | 2010-03-10 | | Release date: | 2010-03-31 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | 22S-Butyl-1alpha,24R-dihydroxyvitamin D(3): Recovery of vitamin D receptor agonistic activity
J.Steroid Biochem.Mol.Biol., 121, 2010
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2Z8R
 | | Crystal structure of rhamnogalacturonan lyase YesW at 1.40 A resolution | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, CALCIUM ION, YesW protein | | Authors: | Ochiai, A, Itoh, T, Maruyama, Y, Kawamata, A, Mikami, B, Hashimoto, W, Murata, K. | | Deposit date: | 2007-09-10 | | Release date: | 2007-10-16 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | A Novel Structural Fold in Polysaccharide Lyases: BACILLUS SUBTILIS FAMILY 11 RHAMNOGALACTURONAN LYASE YesW WITH AN EIGHT-BLADED -PROPELLER
J.Biol.Chem., 282, 2007
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3W91
 | | crystal structure of SeMet-labeled yeast N-acetyltransferase Mpr1 L87M mutant | | Descriptor: | MPR1 protein | | Authors: | Nasuno, R, Hirano, Y, Itoh, T, Hakoshima, T, Hibi, T, Takagi, H. | | Deposit date: | 2013-03-23 | | Release date: | 2013-07-17 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structural and functional analysis of the yeast N-acetyltransferase Mpr1 involved in oxidative stress tolerance via proline metabolism
Proc.Natl.Acad.Sci.USA, 110, 2013
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3W6S
 | | yeast N-acetyltransferase Mpr1 involved in oxidative stress tolerance via proline metabolism | | Descriptor: | HEXAETHYLENE GLYCOL, MAGNESIUM ION, MPR1 protein | | Authors: | Nasuno, R, Hirano, Y, Itoh, T, Hakoshima, T, Hibi, T, Takagi, H. | | Deposit date: | 2013-02-21 | | Release date: | 2013-07-17 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structural and functional analysis of the yeast N-acetyltransferase Mpr1 involved in oxidative stress tolerance via proline metabolism
Proc.Natl.Acad.Sci.USA, 110, 2013
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3WLV
 | | Thermostable urate oxidase from Bacillus sp. TB-90 | | Descriptor: | 8-AZAXANTHINE, CHLORIDE ION, POTASSIUM ION, ... | | Authors: | Hibi, T, Hayashi, Y, Itoh, T. | | Deposit date: | 2013-11-14 | | Release date: | 2014-06-18 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.747 Å) | | Cite: | Intersubunit salt bridges with a sulfate anion control subunit dissociation and thermal stabilization of Bacillus sp. TB-90 urate oxidase.
Biochemistry, 53, 2014
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3WYY
 | | CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH (E)-3-(4-((6-(((3s,5s,7s)-adamantan-1-yl)amino)-4-amino-5-cyanopyridin-2-yl)amino)-2-(cyanomethoxy)phenyl)-N-(2-methoxyethyl)acrylamide | | Descriptor: | (2E)-3-[4-({4-amino-5-cyano-6-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]dec-1-ylamino]pyridin-2-yl}amino)-2-(cyanomethoxy)phenyl]-N-(2-methoxyethyl)prop-2-enamide, Dual specificity protein kinase TTK | | Authors: | Kusakabe, K, Ide, N, Daigo, Y, Itoh, T, Yamamoto, T, Kojima, E, Mitsuoka, Y, Tadano, G, Tagashira, S, Higashino, K, Okano, Y, Sato, Y, Inoue, M, Iguchi, M, Kanazawa, T, Ishioka, Y, Dohi, K, Kido, Y, Sakamoto, S, Ando, S, Maeda, M, Higaki, M, Yoshizawa, H, Murai, H, Nakamura, Y. | | Deposit date: | 2014-09-10 | | Release date: | 2015-04-08 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (3.05 Å) | | Cite: | A unique hinge binder of extremely selective aminopyridine-based Mps1 (TTK) kinase inhibitors with cellular activity.
Bioorg.Med.Chem., 23, 2015
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3WZJ
 | | CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH 4-(6-(cyclohexylamino)-8-(((tetrahydro-2H-pyran-4-yl)methyl)amino)imidazo[1,2-b]pyridazin-3-yl)-N-cyclopropylbenzamide | | Descriptor: | 4-{6-(cyclohexylamino)-8-[(tetrahydro-2H-pyran-4-ylmethyl)amino]imidazo[1,2-b]pyridazin-3-yl}-N-cyclopropylbenzamide, Dual specificity protein kinase TTK | | Authors: | Kusakabe, K, Ide, N, Daigo, Y, Itoh, T, Yamamoto, T, Kojima, E, Mitsuoka, Y, Tadano, G, Tagashira, S, Higashino, K, Okano, Y, Sato, Y, Inoue, M, Iguchi, M, Kanazawa, T, Ishioka, Y, Dohi, K, Kido, Y, Sakamoto, S, Ando, S, Maeda, M, Higaki, M, Yoshizawa, H, Mura, H, Nakamura, Y. | | Deposit date: | 2014-09-29 | | Release date: | 2015-02-11 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.75 Å) | | Cite: | Discovery of imidazo[1,2-b]pyridazine derivatives: selective and orally available Mps1 (TTK) kinase inhibitors exhibiting remarkable antiproliferative activity.
J.Med.Chem., 58, 2015
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3WYX
 | | CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH 6-((3-(cyanomethoxy)-4-(1-methyl-1H-pyrazol-4-yl)phenyl)amino)-2-(cyclohexylamino)nicotinonitrile | | Descriptor: | 6-{[3-(cyanomethoxy)-4-(1-methyl-1H-pyrazol-4-yl)phenyl]amino}-2-(cyclohexylamino)pyridine-3-carbonitrile, Dual specificity protein kinase TTK, IODIDE ION | | Authors: | Kusakabe, K, Ide, N, Daigo, Y, Itoh, T, Yamamoto, T, Kojima, E, Mitsuoka, Y, Tadano, G, Tagashira, S, Higashino, K, Okano, Y, Sato, Y, Inoue, M, Iguchi, M, Kanazawa, T, Ishioka, Y, Dohi, K, Kido, Y, Sakamoto, S, Ando, S, Maeda, M, Higaki, M, Yoshizawa, H, Mura, H, Nakamura, Y. | | Deposit date: | 2014-09-09 | | Release date: | 2015-04-08 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | A unique hinge binder of extremely selective aminopyridine-based Mps1 (TTK) kinase inhibitors with cellular activity.
Bioorg.Med.Chem., 23, 2015
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3WZK
 | | CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH N-cyclopropyl-4-(8-((thiophen-2-ylmethyl)amino)imidazo[1,2-a]pyrazin-3-yl)benzamide | | Descriptor: | CHLORIDE ION, Dual specificity protein kinase TTK, N-cyclopropyl-4-{8-[(thiophen-2-ylmethyl)amino]imidazo[1,2-a]pyrazin-3-yl}benzamide | | Authors: | Kusakabe, K, Ide, N, Daigo, Y, Itoh, T, Yamamoto, T, Kojima, E, Mitsuoka, Y, Tadano, G, Tagashira, S, Higashino, K, Okano, Y, Sato, Y, Inoue, M, Iguchi, M, Kanazawa, T, Ishioka, Y, Dohi, K, Kido, Y, Sakamoto, S, Ando, S, Maeda, M, Higaki, M, Yoshizawa, H, Mura, H, Nakamura, Y. | | Deposit date: | 2014-09-29 | | Release date: | 2015-02-11 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Discovery of imidazo[1,2-b]pyridazine derivatives: selective and orally available Mps1 (TTK) kinase inhibitors exhibiting remarkable antiproliferative activity.
J.Med.Chem., 58, 2015
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2Z8S
 | | Crystal structure of rhamnogalacturonan lyase YesW complexed with digalacturonic acid | | Descriptor: | CALCIUM ION, YesW protein, alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid | | Authors: | Ochiai, A, Itoh, T, Maruyama, Y, Kawamata, A, Mikami, B, Hashimoto, W, Murata, K. | | Deposit date: | 2007-09-10 | | Release date: | 2007-10-16 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | A Novel Structural Fold in Polysaccharide Lyases: BACILLUS SUBTILIS FAMILY 11 RHAMNOGALACTURONAN LYASE YesW WITH AN EIGHT-BLADED -PROPELLER
J.Biol.Chem., 282, 2007
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2ZUX
 | | Crystal structure of rhamnogalacturonan lyase YesW complexed with rhamnose | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, CALCIUM ION, YesW protein, ... | | Authors: | Ochiai, A, Itoh, T, Mikami, B, Hashimoto, W, Murata, K. | | Deposit date: | 2008-10-28 | | Release date: | 2009-02-03 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.32 Å) | | Cite: | Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases
J.Biol.Chem., 284, 2009
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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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6JEY
 | | Covalent bond formation between ynone moiety of synthetic fatty acid and hPPARg-LBD | | Descriptor: | (9Z,12Z,15Z,18Z,21Z)-5-oxidanylidenetetracosa-9,12,15,18,21-pentaen-6-ynoic acid, Peroxisome proliferator-activated receptor gamma | | Authors: | Kojima, H, Yamamoto, K, Itoh, T. | | Deposit date: | 2019-02-07 | | Release date: | 2020-02-12 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Cyclization Reaction-Based Turn-on Probe for Covalent Labeling of Target Proteins.
Cell Chem Biol, 27, 2020
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6JEZ
 | | Covalent labeling of rVDR-LBD by turn-on fluorescent probe mediated by conjugate addition and cyclization | | Descriptor: | (1R,3R)-5-(2-((1R,3aS,7aR,E)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-2- methylenecyclohexane-1,3-diol, 7-(diethylamino)chromen-2-one, Mediator of RNA polymerase II transcription subunit 1, ... | | Authors: | Kojima, H, Yamamoto, K, Itoh, T. | | Deposit date: | 2019-02-07 | | Release date: | 2020-02-12 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Cyclization Reaction-Based Turn-on Probe for Covalent Labeling of Target Proteins.
Cell Chem Biol, 27, 2020
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6JF0
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6IQ5
 | | Crystal Structure of CYP1B1 and Inhibitor Having Azide Group | | Descriptor: | 2-(cis-4-azidocyclohexyl)-4H-naphtho[1,2-b]pyran-4-one, Cytochrome P450 1B1, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Kubo, M, Yamamoto, K, Itoh, T. | | Deposit date: | 2018-11-06 | | Release date: | 2019-01-30 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (3.7 Å) | | Cite: | Design and synthesis of selective CYP1B1 inhibitor via dearomatization of alpha-naphthoflavone.
Bioorg. Med. Chem., 27, 2019
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3VLW
 | | Crystal structure of Sphingomonas sp. A1 alginate-binding protein AlgQ1 in complex with mannuronate-guluronate disaccharide | | Descriptor: | AlgQ1, CALCIUM ION, GLYCEROL, ... | | Authors: | Nishitani, Y, Maruyama, Y, Itoh, T, Mikami, B, Hashimoto, W, Murata, K. | | Deposit date: | 2011-12-05 | | Release date: | 2012-01-25 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Recognition of heteropolysaccharide alginate by periplasmic solute-binding proteins of a bacterial ABC transporter
Biochemistry, 51, 2012
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3VW4
 | | Crystal structure of the DNA-binding domain of ColE2-P9 Rep in complex with the replication origin | | Descriptor: | DNA (5'-D(P*AP*AP*TP*GP*AP*GP*AP*CP*CP*AP*GP*AP*TP*AP*AP*GP*CP*CP*TP*TP*AP*TP*C)-3'), DNA (5'-D(P*GP*AP*TP*AP*AP*GP*GP*CP*TP*TP*AP*TP*CP*TP*GP*GP*TP*CP*TP*CP*AP*TP*T)-3'), Rep, ... | | Authors: | Itou, H, Yagura, M, Itoh, T, Shirakihara, Y. | | Deposit date: | 2012-07-31 | | Release date: | 2013-07-31 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Structural Basis for Replication Origin Unwinding by An Initiator-Primase of Plasmid ColE2-P9: Duplex DNA Unwinding by A Single Protein
J.Biol.Chem., 290, 2015
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2ZUY
 | | Crystal structure of exotype rhamnogalacturonan lyase YesX | | Descriptor: | CALCIUM ION, YesX protein | | Authors: | Ochiai, A, Itoh, T, Mikami, B, Hashimoto, W, Murata, K. | | Deposit date: | 2008-10-28 | | Release date: | 2009-02-03 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases
J.Biol.Chem., 284, 2009
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3VRU
 | | VDR ligand binding domain in complex with 2-Methylidene-19,24-dinor-1alpha,25-dihydroxy vitaminD3 | | Descriptor: | (1R,3R,7E,17beta)-17-[(2R)-5-hydroxy-5-methylhexan-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 (2 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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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
 | | 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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