8IQN
 
 | | Crystal structure of the human vitamin D receptor ligand binding domain complexed with 24,24-F2-25(OH)D3 | | Descriptor: | (1~{S},3~{Z})-3-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R})-5,5-bis(fluoranyl)-6-methyl-6-oxidanyl-heptan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexan-1-ol, Vitamin D3 receptor | | Authors: | Kakuda, S. | | Deposit date: | 2023-03-17 | | Release date: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.639 Å) | | Cite: | Crystal structure of the human vitamin D receptor ligand binding domain complexed with 24,24-F2-25(OH)D3
To Be Published
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8IQT
 | | Crystal structure of the human vitamin D receptor ligand binding domain complexed with (23R)-F-25(OH)D3 | | Descriptor: | (1~{S},3~{Z})-3-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},4~{R})-4-fluoranyl-6-methyl-6-oxidanyl-heptan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexan-1-ol, Vitamin D3 receptor | | Authors: | Kakuda, S. | | Deposit date: | 2023-03-17 | | Release date: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.745 Å) | | Cite: | Crystal structure of the human vitamin D receptor ligand binding domain complexed with (23R)-F-25(OH)D3
To Be Published
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1V84
 | | Crystal structure of human GlcAT-P in complex with N-acetyllactosamine, Udp, and Mn2+ | | Descriptor: | Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1, L(+)-TARTARIC ACID, MANGANESE (II) ION, ... | | Authors: | Kakuda, S, Shiba, T, Ishiguro, M, Tagawa, H, Oka, S, Kajihara, Y, Kawasaki, T, Wakatsuki, S, Kato, R. | | Deposit date: | 2003-12-27 | | Release date: | 2004-05-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.82 Å) | | Cite: | Structural Basis for Acceptor Substrate Recognition of a Human Glucuronyltransferase, GlcAT-P, an Enzyme Critical in the Biosynthesis of the Carbohydrate Epitope HNK-1
J.Biol.Chem., 279, 2004
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1V83
 | | Crystal structure of human GlcAT-P in complex with Udp and Mn2+ | | Descriptor: | Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1, L(+)-TARTARIC ACID, MANGANESE (II) ION, ... | | Authors: | Kakuda, S, Shiba, T, Ishiguro, M, Tagawa, H, Oka, S, Kajihara, Y, Kawasaki, T, Wakatsuki, S, Kato, R. | | Deposit date: | 2003-12-27 | | Release date: | 2004-05-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structural Basis for Acceptor Substrate Recognition of a Human Glucuronyltransferase, GlcAT-P, an Enzyme Critical in the Biosynthesis of the Carbohydrate Epitope HNK-1
J.Biol.Chem., 279, 2004
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1V82
 | | Crystal structure of human GlcAT-P apo form | | Descriptor: | Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1, L(+)-TARTARIC ACID | | Authors: | Kakuda, S, Shiba, T, Ishiguro, M, Tagawa, H, Oka, S, Kajihara, Y, Kawasaki, T, Wakatsuki, S, Kato, R. | | Deposit date: | 2003-12-27 | | Release date: | 2004-05-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Structural Basis for Acceptor Substrate Recognition of a Human Glucuronyltransferase, GlcAT-P, an Enzyme Critical in the Biosynthesis of the Carbohydrate Epitope HNK-1
J.Biol.Chem., 279, 2004
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5Y1A
 | | HBP35 of Porphyromonas gingivalis | | Descriptor: | 35 kDa hemin binding protein | | Authors: | Kakuda, S, Suzuki, M, Sato, K. | | Deposit date: | 2017-07-20 | | Release date: | 2018-07-25 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Immunoglobulin-like domains of the cargo proteins are essential for protein stability during secretion by the type IX secretion system.
Mol. Microbiol., 110, 2018
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4ITF
 | | Crystal structure of the human vitamin D receptor ligand binding domain complexed with 1alpha,25-Dihydroxy-2alpha-[2-(1H-tetrazole-1-yl)ethyl]vitamin D3 | | Descriptor: | (1R,2S,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-2-[2-(1,2,3,4-tetrazol-1-yl)ethyl]cyclohexane-1,3-diol, Vitamin D3 receptor | | Authors: | Kakuda, S, Takimoto-Kamimura, M. | | Deposit date: | 2013-01-18 | | Release date: | 2014-01-22 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.84 Å) | | Cite: | Synthesis of 2 alpha-heteroarylalkyl active vitamin d3 with therapeutic effect on enhancing bone mineral density in vivo
ACS MED.CHEM.LETT., 4, 2013
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4ITE
 | | Crystal structure of the human vitamin D receptor ligand binding domain complexed with 1alpha,25-Dihydroxy-2alpha-[2-(2H-tetrazol-2-yl)ethyl]vitamin D3 | | Descriptor: | (1R,2S,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-2-[2-(1,2,3,4-tetrazol-2-yl)ethyl]cyclohexane-1,3-diol, Vitamin D3 receptor | | Authors: | Kakuda, S, Takimoto-Kamimura, M. | | Deposit date: | 2013-01-18 | | Release date: | 2014-01-22 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.49 Å) | | Cite: | Synthesis of 2 alpha-heteroarylalkyl active vitamin d3 with therapeutic effect on enhancing bone mineral density in vivo
ACS MED.CHEM.LETT., 4, 2013
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4KP0
 | | Crystal Structure of the human Chymase with TJK002 | | Descriptor: | 4-({1-[(4-methyl-1-benzothiophen-3-yl)methyl]-1H-benzimidazol-2-yl}sulfanyl)butanoic acid, Chymase | | Authors: | Kakuda, S, Takimoto-Kamimura, M. | | Deposit date: | 2013-05-12 | | Release date: | 2013-10-30 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystal structure of a complex of human chymase with its benzimidazole derived inhibitor
J.SYNCHROTRON RADIAT., 20, 2013
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3VHW
 | | Crystal structure of the human vitamin D receptor ligand binding domain complexed with 4-MP | | Descriptor: | Vitamin D3 receptor, methyl (1S,3E)-3-{(2R)-2-[(1R,3aS,4E,7aR)-4-{(2Z)-2-[(3R,4S,5R)-3,5-dihydroxy-4-(3-hydroxypropoxy)-2-methylidenecyclohexylidene]ethylidene}-7a-methyloctahydro-1H-inden-1-yl]propylidene}-1-ethyl-2-oxocyclopentanecarboxylate (non-preferred name) | | Authors: | Kakuda, S, Takimoto-Kamimura, M. | | Deposit date: | 2011-09-08 | | Release date: | 2013-03-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.43 Å) | | Cite: | Synthesis of novel C-2 substituted vitamin D derivatives having ringed side chains and their biological evaluation on bone
J.Steroid Biochem.Mol.Biol., 136, 2013
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3WWR
 | | Crystal structure of the human vitamin D receptor ligand binding domain complexed with 1-((((1S,2R,6R,Z)-2,6-dihydroxy-4-((E)-2-((1R,3aS,7aR)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methylhexahydro-1H-inden-4(2H)-ylidene)ethylidene)-3-methylenecyclohexyl)oxy)methyl)cyclopropanecarbonitrile | | Descriptor: | 1-({[(1R,2S,3R,5Z,7E,14beta,17alpha)-1,3,25-trihydroxy-9,10-secocholesta-5,7,10-trien-2-yl]oxy}methyl)cyclopropanecarbonitrile, Vitamin D3 receptor | | Authors: | Kakuda, S, Takimoto-Kamimura, M. | | Deposit date: | 2014-06-27 | | Release date: | 2014-12-31 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.18 Å) | | Cite: | Synthesis and biological activities of vitamin D3 derivatives with cyanoalkyl side chain at C-2 position.
J.Steroid Biochem.Mol.Biol., 148, 2015
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3X31
 | | Crystal structure of the human vitamin D receptor ligand binding domain complexed with 7,8-cis-14-epi-1a,25-Dihydroxy-19-norvitamin D3 | | Descriptor: | (1R,3R,7Z,14beta,17alpha)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9,10-secoestra-5,7-diene-1,3-diol, Vitamin D3 receptor | | Authors: | Kakuda, S, Takimoto-Kamimura, M. | | Deposit date: | 2015-01-13 | | Release date: | 2016-01-13 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.11 Å) | | Cite: | Revisiting the 7,8-cis-vitamin D3 derivatives: synthesis, evaluating the biological activity, and study of the binding configuration
To be Published
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3A2J
 | | Crystal structure of the human vitamin D receptor (H305F/H397F) ligand binding domain complexed with TEI-9647 | | Descriptor: | (1S,3R,5Z,7E,20S,23S)-1,3-dihydroxy-23,26-epoxy-9,10-secocholesta-5,7,10,25(27)-tetraen-26-one, Vitamin D3 receptor | | Authors: | Kakuda, S, Takimoto-Kamimura, M. | | Deposit date: | 2009-05-20 | | Release date: | 2010-05-26 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Structural basis of the histidine-mediated vitamin D receptor agonistic and antagonistic mechanisms of (23S)-25-dehydro-1alpha-hydroxyvitamin D(3)-26,23-lactone
Acta Crystallogr.,Sect.D, 66, 2010
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3A2H
 | | Crystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205 | | Descriptor: | (1S,3R,5Z,7E,20S,23S)-1,3-dihydroxy-23,26-epoxy-9,10-secocholesta-5,7,10,25(27)-tetraen-26-one, Mediator of RNA polymerase II transcription subunit 1 peptide, Vitamin D3 receptor | | Authors: | Kakuda, S, Takimoto-Kamimura, M. | | Deposit date: | 2009-05-20 | | Release date: | 2010-05-26 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structural basis of the histidine-mediated vitamin D receptor agonistic and antagonistic mechanisms of (23S)-25-dehydro-1alpha-hydroxyvitamin D(3)-26,23-lactone
Acta Crystallogr.,Sect.D, 66, 2010
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3AX8
 | | Crystal structure of the human vitamin D receptor ligand binding domain complexed with 15alpha-methoxy-1alpha,25-dihydroxyvitamin D3 | | Descriptor: | (1R,3S,5Z)-5-[(2E)-2-[(1R,3S,3aS,7aR)-1-[(2R)-6-hydroxy-6-methyl-heptan-2-yl]-3-methoxy-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol, Vitamin D3 receptor | | Authors: | Kakuda, S, Takimoto-Kamimura, M. | | Deposit date: | 2011-03-30 | | Release date: | 2011-10-05 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | New C15-substituted active vitamin D3
Org.Lett., 13, 2011
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3A2I
 | | Crystal structure of the human vitamin D receptor (H305F) ligand binding domain complexed with TEI-9647 | | Descriptor: | (1S,3R,5Z,7E,20S,23S)-1,3-dihydroxy-23,26-epoxy-9,10-secocholesta-5,7,10,25(27)-tetraen-26-one, Vitamin D3 receptor | | Authors: | Kakuda, S, Takimoto-Kamimura, M. | | Deposit date: | 2009-05-20 | | Release date: | 2010-05-26 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (3.27 Å) | | Cite: | Structural basis of the histidine-mediated vitamin D receptor agonistic and antagonistic mechanisms of (23S)-25-dehydro-1alpha-hydroxyvitamin D(3)-26,23-lactone
Acta Crystallogr.,Sect.D, 66, 2010
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2ZFX
 | | Crystal structure of the rat vitamin D receptor ligand binding domain complexed with YR301 and a synthetic peptide containing the NR2 box of DRIP 205 | | Descriptor: | (2S)-3-{4-[1-ethyl-1-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)propyl]-2-methylphenoxy}propane-1,2-diol, DRIP 205 NR2 box peptide, Vitamin D3 receptor | | Authors: | Kakuda, S, Takimoto-Kamimura, M. | | Deposit date: | 2008-01-15 | | Release date: | 2009-01-20 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.99 Å) | | Cite: | Structure of the ligand-binding domain of rat VDR in complex with the nonsecosteroidal vitamin D3 analogue YR301
Acta Crystallogr.,Sect.F, 64, 2008
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3AUQ
 | | Crystal structure of the human vitamin D receptor ligand binding domain complexed with Yne-diene type analog of active 14-epi-2alpha-methyl-19-norvitamin D3 | | Descriptor: | (1R,2S,3R)-5-[2-[(1R,3aS,7aR)-1-[(2R)-6-hydroxy-6-methyl-heptan-2-yl]-7a-methyl-1,2,3,3a,6,7-hexahydroinden-4-yl]ethynyl]-2-methyl-cyclohex-4-ene-1,3-diol, Vitamin D3 receptor | | Authors: | Kakuda, S, Takimoto-Kamimura, M. | | Deposit date: | 2011-02-15 | | Release date: | 2011-09-14 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.64 Å) | | Cite: | Development of 14-epi-19-nortachysterol and its unprecedented binding configuration for the human vitamin D receptor
J.Am.Chem.Soc., 133, 2011
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3AUR
 | | Crystal structure of the human vitamin D receptor ligand binding domain complexed with Yne-diene type analog of active 14-epi-2beta-methyl-19-norvitamin D3 | | Descriptor: | (1R,2S,3R)-5-[2-[(1R,3aS,7aR)-1-[(2R)-6-hydroxy-6-methyl-heptan-2-yl]-7a-methyl-1,2,3,3a,6,7-hexahydroinden-4-yl]ethynyl]-2-methyl-cyclohex-4-ene-1,3-diol, Vitamin D3 receptor | | Authors: | Kakuda, S, Takimoto-Kamimura, M. | | Deposit date: | 2011-02-15 | | Release date: | 2011-09-14 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.21 Å) | | Cite: | Development of 14-epi-19-nortachysterol and its unprecedented binding configuration for the human vitamin D receptor
J.Am.Chem.Soc., 133, 2011
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3AUN
 | | Crystal structure of the rat vitamin D receptor ligand binding domain complexed with YR335 and a synthetic peptide containing the NR2 box of DRIP 205 | | Descriptor: | (2R)-2-{4-[3-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)pentan-3-yl]-2-methylphenoxy}butane-1,4-diol, DRIP 205 NR2 box peptide, Vitamin D3 receptor | | Authors: | Kakuda, S, Takimoto-Kamimura, M. | | Deposit date: | 2011-02-10 | | Release date: | 2012-02-15 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.81 Å) | | Cite: | Design, synthesis and X-ray crystallographic study of new nonsecosteroidal vitamin D receptor ligands
Bioorg.Med.Chem.Lett., 21, 2011
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2D0J
 | | Crystal Structure of Human GlcAT-S Apo Form | | Descriptor: | Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2 | | Authors: | Shiba, T, Kakuda, S, Ishiguro, M, Oka, S, Kawasaki, T, Wakatsuki, S, Kato, R. | | Deposit date: | 2005-08-03 | | Release date: | 2006-07-18 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structure of GlcAT-S, a human glucuronyltransferase, involved in the biosynthesis of the HNK-1 carbohydrate epitope
To be published
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5YSY
 | | Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2R,3R)-5-[(E)-2-{(1R,3aS,7aR)-1-[(R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-2,3,3a,6,7,7a-hexahydro-1H-inden-4-yl}vinyl]-2-(3-hydroxypropyl)cyclohex-4-ene-1,3-diol | | Descriptor: | (1R,2R,3R)-5-[(E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-1,2,3,3a,6,7-hexahydroinden-4-yl]e thenyl]-2-(3-oxidanylpropyl)cyclohex-4-ene-1,3-diol, Vitamin D3 receptor | | Authors: | Takimoto-Kamimura, M, Kakuda, S. | | Deposit date: | 2017-11-16 | | Release date: | 2018-04-11 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Effects of 2-substitution on 14-epi-19-nortachysterol-mediated biological events: based on synthesis and X-ray co-crystallographic analysis with the human vitamin D receptor.
Org. Biomol. Chem., 16, 2018
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5YT2
 | | Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R)-5-[(E)-2-{(1R,3aS,7aR)-1-[(R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-2,3,3a,6,7,7a-hexahydro-1H-inden-4-yl}vinyl]-2-(3-hydroxypropyl)cyclohex-4-ene-1,3-diol | | Descriptor: | (1R,2S,3R)-5-[(E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-1,2,3,3a,6,7-hexahydroinden-4-yl]ethenyl]-2-(3-oxidanylpropyl)cyclohex-4-ene-1,3-diol, Vitamin D3 receptor | | Authors: | Takimoto-Kamimura, M, Kakuda, S. | | Deposit date: | 2017-11-16 | | Release date: | 2018-04-11 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Effects of 2-substitution on 14-epi-19-nortachysterol-mediated biological events: based on synthesis and X-ray co-crystallographic analysis with the human vitamin D receptor.
Org. Biomol. Chem., 16, 2018
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3X36
 | | Crystal structure of the human vitamin D receptor ligand binding domain complexed with 7,8-cis-1a,25-Dihydroxy-19-norvitamin D3 | | Descriptor: | (1R,3R)-5-[(2Z)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]cyclohexane-1,3-diol, Vitamin D3 receptor | | Authors: | Takimoto-Kamimura, M, Kakuda, S. | | Deposit date: | 2015-01-16 | | Release date: | 2016-01-20 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.93 Å) | | Cite: | Revisiting the 7,8-cis-vitamin D3 derivatives: synthesis, evaluating the biological activity, and study of the binding configuration
To be Published
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