5AWK
| Crystal structure of VDR-LBD/partial agonist complex: 22S-ethyl analogue | Descriptor: | (1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,3S)-3-ethyl-5-oxidanyl-pentan-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, Yamamoto, K. | Deposit date: | 2015-07-04 | Release date: | 2015-11-18 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.9 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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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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5AZV
| Crystal structure of hPPARgamma ligand binding domain complexed with 17-oxoDHA | Descriptor: | (4~{Z},7~{Z},10~{Z},13~{Z},19~{Z})-17-oxidanylidenedocosa-4,7,10,13,19-pentaenoic acid, Peroxisome proliferator-activated receptor gamma | Authors: | Egawa, D, Itoh, T, Yamamoto, K. | Deposit date: | 2015-10-23 | Release date: | 2016-07-06 | Last modified: | 2024-10-23 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | 17-OxoDHA Is a PPAR alpha/gamma Dual Covalent Modifier and Agonist Acs Chem.Biol., 2016
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5B41
| Crystal structure of VDR-LBD complexed with 2-methylidene-19-nor-1a,25-dihydroxyvitamin D3 | 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, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | Authors: | Anami, Y, Itoh, T, Yamamoto, K. | Deposit date: | 2016-03-23 | Release date: | 2016-12-07 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.89 Å) | Cite: | Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by Hybrid Approach Combining Small-Angle X-ray Scattering and Molecular Dynamics J.Med.Chem., 59, 2016
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5B5B
| Crystal structure of VDR-LBD complexed with 2-methylidene-26,27-diphenyl-19-nor-1,25-dihydroxyvitamin D3 | Descriptor: | (1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-oxidanyl-7-phenyl-6-(phenylmethyl)heptan-2-yl]-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 | Authors: | Kato, A, Itoh, T, Yamamoto, K. | Deposit date: | 2016-05-02 | Release date: | 2016-06-29 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Helix12-Stabilization Antagonist of Vitamin D Receptor Bioconjug.Chem., 27, 2016
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7E2O
| X-ray Crystal structure of PPARgamma R288H mutant. | Descriptor: | Peroxisome proliferator-activated receptor gamma | Authors: | Egawa, D, Itoh, T. | Deposit date: | 2021-02-06 | Release date: | 2022-01-19 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Structural Insights into the Loss-of-Function R288H Mutant of Human PPAR gamma. Biol.Pharm.Bull., 44, 2021
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5XUQ
| Crystal structure of VDR-LBD complexed with an antagonist, 2-methylidene-19,26,27-trinor-22-(S)-butyl-1-hydroxy-25-oxo-25-(1H-pyrrol-2-yl)- vitamin D3 | Descriptor: | (4~{S})-4-[(1~{R})-1-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]ethyl]-1-(1~{H}-pyrrol-2-yl)octan-1-one, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | Authors: | Kato, A, Itoh, T, Yamamoto, K. | Deposit date: | 2017-06-24 | Release date: | 2018-06-27 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Discovery of Potent Vitamin D Receptor Antagonist To Be Published
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2E9Q
| Recombinant pro-11S globulin of pumpkin | Descriptor: | 11S globulin subunit beta, CHLORIDE ION, PHOSPHATE ION | Authors: | Fukuda, T, Prak, K, Itoh, T, Masuda, T, Maruyama, N, Mikami, B, Utsumi, S. | Deposit date: | 2007-01-26 | Release date: | 2008-02-26 | Last modified: | 2024-10-23 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Conservation and divergence on plant seed 11S globulins based on crystal structures. Biochim.Biophys.Acta, 2010
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7EFQ
| Crystal structure of hPPARgamma ligand binding domain complexed with rosiglitazone-based fluorescence probe | Descriptor: | (5S)-5-[[4-[2-[[7-(diethylamino)-2-oxidanylidene-chromen-4-yl]-methyl-amino]ethoxy]phenyl]methyl]-1,3-thiazolidine-2,4-dione, Peroxisome proliferator-activated receptor gamma | Authors: | Yoshikawa, C, Ishida, H, Ohashi, N, Itoh, T. | Deposit date: | 2021-03-23 | Release date: | 2021-05-12 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Synthesis of a Coumarin-Based PPAR gamma Fluorescence Probe for Competitive Binding Assay. Int J Mol Sci, 22, 2021
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5ZWI
| Interaction between Vitamin D receptor (VDR) and a ligand having a dienone group | Descriptor: | (2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-4,6-diene-3-one, 13-meric peptide from DRIP205 NR2 BOX peptide, Vitamin D3 receptor | Authors: | Yoshizawa, M, Itoh, T, Anami, Y, Kato, A, Yoshimoto, N, Yamamoto, K. | Deposit date: | 2018-05-15 | Release date: | 2018-07-18 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands J. Med. Chem., 61, 2018
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5ZWH
| Covalent bond formation between histidine of Vitamin D receptor (VDR) and a full agonist having an ene-ynone group via conjugate addition reaction | Descriptor: | (2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-4,6-diene-3-one, (E,2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-6-en-4-yn-3-one, 13-meric peptide from DRIP205 NR2 BOX peptide, ... | Authors: | Yoshizawa, M, Itoh, T, Anami, Y, Kato, A, Yoshimoto, N, Yamamoto, K. | Deposit date: | 2018-05-15 | Release date: | 2018-07-18 | Last modified: | 2024-10-23 | Method: | X-RAY DIFFRACTION (2.38 Å) | Cite: | Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands J. Med. Chem., 61, 2018
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5ZJG
| Gamma-glutamyltranspeptidase from Pseudomonas nitroreducens complexed with Gly-Gly | Descriptor: | GLYCEROL, GLYCINE, Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03 L-subunit, ... | Authors: | Hibi, T, Imaoka, M, Itoh, T, Wakayama, M. | Deposit date: | 2018-03-20 | Release date: | 2019-01-16 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.702 Å) | Cite: | Crystal structure analysis and enzymatic characterization of gamma-glutamyltranspeptidase from Pseudomonas nitroreducens. Biosci. Biotechnol. Biochem., 83, 2019
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5ZWE
| Covalent bond formation between histidine of Vitamin D receptor (VDR) and a full agonist having a vinyl ketone group via conjugate addition reaction | Descriptor: | (6R)-6-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]hept-1-en-3-one, 13-meric peptide from DRIP205 NR2 BOX peptide, Vitamin D3 receptor | Authors: | Yoshizawa, M, Itoh, T, Anami, Y, Kato, A, Yoshimoto, N, Yamamoto, K. | Deposit date: | 2018-05-15 | Release date: | 2018-07-18 | Last modified: | 2018-08-08 | Method: | X-RAY DIFFRACTION (2.72 Å) | Cite: | Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands J. Med. Chem., 61, 2018
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6A6U
| Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with R61G mutation, in complex with FSA | Descriptor: | (4S,5S)-1,2-DITHIANE-4,5-DIOL, 1-S-(carboxymethyl)-1-thio-beta-D-fructopyranose, FLAVIN-ADENINE DINUCLEOTIDE, ... | Authors: | Ogawa, N, Maruyama, Y, Itoh, T, Hashimoto, W, Murata, K. | Deposit date: | 2018-06-29 | Release date: | 2019-05-15 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.945 Å) | Cite: | Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis. Sci Rep, 9, 2019
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6A6T
| Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with R61G mutation | Descriptor: | (4S,5S)-1,2-DITHIANE-4,5-DIOL, FLAVIN-ADENINE DINUCLEOTIDE, Fructosyl amine: oxygen oxidoreductase, ... | Authors: | Ogawa, N, Maruyama, Y, Itoh, T, Hashimoto, W, Murata, K. | Deposit date: | 2018-06-29 | Release date: | 2019-05-15 | Last modified: | 2024-10-30 | Method: | X-RAY DIFFRACTION (1.901 Å) | Cite: | Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis. Sci Rep, 9, 2019
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6A6V
| Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with 7 additional mutations, in complex with FSA | Descriptor: | 1-S-(carboxymethyl)-1-thio-beta-D-fructopyranose, FLAVIN-ADENINE DINUCLEOTIDE, Fructosyl amine: oxygen oxidoreductase | Authors: | Ogawa, N, Maruyama, Y, Itoh, T, Hashimoto, W, Murata, K. | Deposit date: | 2018-06-29 | Release date: | 2019-05-15 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis. Sci Rep, 9, 2019
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6A6R
| Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans, Seleno-methionine Derivative | Descriptor: | (4S,5S)-1,2-DITHIANE-4,5-DIOL, FLAVIN-ADENINE DINUCLEOTIDE, Fructosyl amine: oxygen oxidoreductase, ... | Authors: | Ogawa, N, Maruyama, Y, Itoh, T, Hashimoto, W, Murata, K. | Deposit date: | 2018-06-29 | Release date: | 2019-05-15 | Method: | X-RAY DIFFRACTION (2.609 Å) | Cite: | Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis. Sci Rep, 9, 2019
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6A6S
| Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans in complex with FSA, Seleno-methionine Derivative | Descriptor: | (4S,5S)-1,2-DITHIANE-4,5-DIOL, 1-S-(carboxymethyl)-1-thio-beta-D-fructopyranose, FLAVIN-ADENINE DINUCLEOTIDE, ... | Authors: | Ogawa, N, Maruyama, Y, Itoh, T, Hashimoto, W, Murata, K. | Deposit date: | 2018-06-29 | Release date: | 2019-05-15 | Last modified: | 2024-10-30 | Method: | X-RAY DIFFRACTION (1.851 Å) | Cite: | Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis. Sci Rep, 9, 2019
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5ZWF
| Covalent bond formation between histidine of Vitamin D receptor (VDR) and a full agonist having a enone with a beta methyl group via conjugate addition reaction | Descriptor: | (E,7R)-7-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-2-en-4-one, 13-meric peptide from DRIP205 NR2 BOX peptide, Vitamin D3 receptor | Authors: | Yoshizawa, M, Itoh, T, Anami, Y, Kato, A, Yoshimoto, N, Yamamoto, K. | Deposit date: | 2018-05-15 | Release date: | 2018-07-18 | Last modified: | 2018-08-08 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands J. Med. Chem., 61, 2018
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5XPL
| Crystal structure of VDR-LBD complexed with 22S-butyl-25-hydroxyphenyl-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3 | Descriptor: | (4~{S})-4-[(1~{R})-1-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl )cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]ethyl]-1-(4-hydroxyphenyl)octan-1-one, Nuclear receptor coactivator 2, Vitamin D3 receptor | Authors: | Kato, A, Itoh, T, Yamamoto, K. | Deposit date: | 2017-06-03 | Release date: | 2018-06-06 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.05 Å) | Cite: | Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action J. Med. Chem., 60, 2017
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5XPM
| Crystal structure of VDR-LBD complexed with 22S-Butyl-25RS-(hydroxyphenyl)-25-methoxy-2-methylidene-19,26,27-trinor-1-hydroxyvitamin D3 | Descriptor: | (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},3~{S})-3-[(3~{S})-3-(4-hydroxyphenyl)-3-methoxy-propyl]heptan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | Authors: | Kato, A, Itoh, T, Yamamoto, K. | Deposit date: | 2017-06-03 | Release date: | 2018-06-06 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action J. Med. Chem., 60, 2017
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5XPN
| Crystal structure of VDR-LBD complexed with 25RS-(hydroxyphenyl)-25-methoxy-2-methylidene-19,26,27-trinor-1-hydroxyvitamin D3 | Descriptor: | (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{R})-6-(4-hydroxyphenyl)-6-methoxy-hexan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol, (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{S})-6-(4-hydroxyphenyl)-6-methoxy-hexan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, ... | Authors: | Kato, A, Itoh, T, Yamamoto, K. | Deposit date: | 2017-06-03 | Release date: | 2018-07-11 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.96 Å) | Cite: | Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action J. Med. Chem., 60, 2017
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5XPP
| Crystal structure of VDR-LBD complexed with 25RS-(Hydroxyphenyl)-2-methylidene-19,26,27-trinor-1,25-dihydroxyvitamin D3 | Descriptor: | (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{R})-6-(4-hydroxyphenyl)-6-oxidanyl-hexan-2-yl]-7~{ a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | Authors: | Kato, A, Itoh, T, Yamamoto, K. | Deposit date: | 2017-06-03 | Release date: | 2018-06-06 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.85 Å) | Cite: | Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action J. Med. Chem., 60, 2017
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5XPO
| Crystal structure of VDR-LBD complexed with 25-(hydroxyphenyl)-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3 | Descriptor: | (5~{R})-5-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl)cyclohexyl idene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]-1-(4-hydroxyphenyl)hexan-1-one, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | Authors: | Kato, A, Itoh, T, Yamamoto, K. | Deposit date: | 2017-06-03 | Release date: | 2018-06-06 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.28 Å) | Cite: | Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action J. Med. Chem., 60, 2017
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3VQU
| CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH 4-[(4-amino-5-cyano-6-ethoxypyridin-2- yl)amino]benzamide | Descriptor: | 4-[(4-amino-5-cyano-6-ethoxypyridin-2-yl)amino]benzamide, Dual specificity protein kinase TTK, IODIDE ION | Authors: | Kusakabe, K, Ide, N, Daigo, Y, Itoh, T, Higashino, K, Okano, Y, Tadano, G, Tachibana, Y, Sato, Y, Inoue, M, Wada, T, Iguchi, M, Kanazawa, T, Ishioka, Y, Dohi, K, Tagashira, S, Kido, Y, Sakamoto, S, Yasuo, K, Maeda, M, Yamamoto, T, Higaki, M, Endoh, T, Ueda, K, Shiota, T, Murai, H, Nakamura, Y. | Deposit date: | 2012-03-30 | Release date: | 2012-06-27 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Diaminopyridine-based potent and selective mps1 kinase inhibitors binding to an unusual flipped-Peptide conformation. Acs Med.Chem.Lett., 3, 2012
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