Author results

1V82
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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:2011-07-13
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
1V83
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CRYSTAL STRUCTURE OF HUMAN GLCAT-P IN COMPLEX WITH UDP AND MN2+
Descriptor:Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1, MANGANESE (II) ION, 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:2011-07-13
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
1V84
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CRYSTAL STRUCTURE OF HUMAN GLCAT-P IN COMPLEX WITH N-ACETYLLACTOSAMINE, UDP, AND MN2+
Descriptor:Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1, BETA-D-GALACTOSE, 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE, ...
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:2011-07-13
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
3A2H
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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:Vitamin D3 receptor, Mediator of RNA polymerase II transcription subunit 1 peptide, (1S,3R,5Z,7E,20S,23S)-1,3-dihydroxy-23,26-epoxy-9,10-secocholesta-5,7,10,25(27)-tetraen-26-one
Authors:Kakuda, S., Takimoto-Kamimura, M.
Deposit date:2009-05-20
Release date:2010-05-26
Last modified:2017-08-09
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
3A2I
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CRYSTAL STRUCTURE OF THE HUMAN VITAMIN D RECEPTOR (H305F) LIGAND BINDING DOMAIN COMPLEXED WITH TEI-9647
Descriptor:Vitamin D3 receptor, (1S,3R,5Z,7E,20S,23S)-1,3-dihydroxy-23,26-epoxy-9,10-secocholesta-5,7,10,25(27)-tetraen-26-one
Authors:Kakuda, S., Takimoto-Kamimura, M.
Deposit date:2009-05-20
Release date:2010-05-26
Last modified:2017-08-09
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
3A2J
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CRYSTAL STRUCTURE OF THE HUMAN VITAMIN D RECEPTOR (H305F/H397F) LIGAND BINDING DOMAIN COMPLEXED WITH TEI-9647
Descriptor:Vitamin D3 receptor, (1S,3R,5Z,7E,20S,23S)-1,3-dihydroxy-23,26-epoxy-9,10-secocholesta-5,7,10,25(27)-tetraen-26-one
Authors:Kakuda, S., Takimoto-Kamimura, M.
Deposit date:2009-05-20
Release date:2010-05-26
Last modified:2017-08-09
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
2ZFX
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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:Vitamin D3 receptor, DRIP 205 NR2 box peptide, (2S)-3-{4-[1-ethyl-1-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)propyl]-2-methylphenoxy}propane-1,2-diol
Authors:Kakuda, S., Takimoto-Kamimura, M.
Deposit date:2008-01-15
Release date:2009-01-20
Last modified:2017-08-23
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
3AX8
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CRYSTAL STRUCTURE OF THE HUMAN VITAMIN D RECEPTOR LIGAND BINDING DOMAIN COMPLEXED WITH 15ALPHA-METHOXY-1ALPHA,25-DIHYDROXYVITAMIN D3
Descriptor:Vitamin D3 receptor, (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
Authors:Kakuda, S., Takimoto-Kamimura, M.
Deposit date:2011-03-30
Release date:2011-10-05
Last modified:2017-08-16
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:New C15-substituted active vitamin D3
Org.Lett., 13, 2011
3AUN
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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:Vitamin D3 receptor, DRIP 205 NR2 box peptide, (2R)-2-{4-[3-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)pentan-3-yl]-2-methylphenoxy}butane-1,4-diol
Authors:Kakuda, S., Takimoto-Kamimura, M.
Deposit date:2011-02-10
Release date:2012-02-15
Last modified:2017-08-23
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
3AUQ
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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:Vitamin D3 receptor, (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
Authors:Kakuda, S., Takimoto-Kamimura, M.
Deposit date:2011-02-15
Release date:2011-09-14
Last modified:2017-08-16
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
3AUR
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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:Vitamin D3 receptor, (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
Authors:Kakuda, S., Takimoto-Kamimura, M.
Deposit date:2011-02-15
Release date:2011-09-14
Last modified:2017-08-16
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
3VHW
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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:2017-08-16
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
3WWR
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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:Vitamin D3 receptor, 1-({[(1R,2S,3R,5Z,7E,14beta,17alpha)-1,3,25-trihydroxy-9,10-secocholesta-5,7,10-trien-2-yl]oxy}methyl)cyclopropanecarbonitrile
Authors:Kakuda, S., Takimoto-Kamimura, M.
Deposit date:2014-06-27
Release date:2014-12-31
Last modified:2017-08-16
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., 2014
3X31
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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:Vitamin D3 receptor, (1R,3R,7Z,14beta,17alpha)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9,10-secoestra-5,7-diene-1,3-diol
Authors:Kakuda, S., Takimoto-Kamimura, M.
Deposit date:2015-01-13
Release date:2016-01-13
Last modified:2017-08-23
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
4ITE
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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:Vitamin D3 receptor, (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
Authors:Kakuda, S., Takimoto-Kamimura, M.
Deposit date:2013-01-18
Release date:2014-01-22
Last modified:2017-08-16
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
4ITF
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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:Vitamin D3 receptor, (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
Authors:Kakuda, S., Takimoto-Kamimura, M.
Deposit date:2013-01-18
Release date:2014-01-22
Last modified:2017-08-16
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
4KP0
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CRYSTAL STRUCTURE OF THE HUMAN CHYMASE WITH TJK002
Descriptor:Chymase, 4-({1-[(4-methyl-1-benzothiophen-3-yl)methyl]-1H-benzimidazol-2-yl}sulfanyl)butanoic acid
Authors:Kakuda, S., Takimoto-Kamimura, M.
Deposit date:2013-05-12
Release date:2013-10-30
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
5Y1A
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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:2019-02-06
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
2D0J
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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:2011-07-13
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
3X36
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CRYSTAL STRUCTURE OF THE HUMAN VITAMIN D RECEPTOR LIGAND BINDING DOMAIN COMPLEXED WITH 7,8-CIS-1A,25-DIHYDROXY-19-NORVITAMIN D3
Descriptor:Vitamin D3 receptor, (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
Authors:Takimoto-Kamimura, M., Kakuda, S.
Deposit date:2015-01-16
Release date:2016-01-20
Last modified:2017-08-23
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
5YSY
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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:Vitamin D3 receptor, (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]ethenyl]-2-(3-oxidanylpropyl)cyclohex-4-ene-1,3-diol
Authors:Takimoto-Kamimura, M., Kakuda, S.
Deposit date:2017-11-16
Release date:2018-04-11
Last modified:2018-04-18
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
5YT2
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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:Vitamin D3 receptor, (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
Authors:Takimoto-Kamimura, M., Kakuda, S.
Deposit date:2017-11-16
Release date:2018-04-11
Last modified:2018-04-18
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
5UK5
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COMPLEX OF NOTCH1(EGF8-12) BOUND TO JAGGED1(N-EGF3)
Descriptor:Neurogenic locus notch homolog protein 1, Protein jagged-1, CALCIUM ION, ...
Authors:Garcia, K.C., Luca, V.C.
Deposit date:2017-01-19
Release date:2017-03-08
Last modified:2018-01-24
Method:X-RAY DIFFRACTION (2.506 Å)
Cite:Notch-Jagged complex structure implicates a catch bond in tuning ligand sensitivity.
Science, 355, 2017