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PDB: 146 件
7CUG
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Crystal Structure of Urate Oxidase from Bacillus sp. TB-90 in the absence from Chloride Anion at 1.62 A resolution
分子名称: 2-METHOXYETHANOL, 8-AZAXANTHINE, OXYGEN MOLECULE, ...
著者Hibi, T, Itoh, T.
登録日2020-08-23
公開日2020-11-25
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.62 Å)
主引用文献Identification of quasi-stable water molecules near the Thr73-Lys13 catalytic diad of Bacillus sp. TB-90 urate oxidase by X-ray crystallography with controlled humidity.
J.Biochem., 169, 2021
5AWJ
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Crystal structure of VDR-LBD/partial agonist complex: 22S-hexyl analogue
分子名称: (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
著者Anami, Y, Itoh, T, Inaba, Y, Nakabayashi, M, Ikura, T, Ito, N, Yamamoto, K.
登録日2015-07-04
公開日2015-11-18
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献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
5AWK
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Crystal structure of VDR-LBD/partial agonist complex: 22S-ethyl analogue
分子名称: (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
著者Anami, Y, Itoh, T, Yamamoto, K.
登録日2015-07-04
公開日2015-11-18
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (2.9 Å)
主引用文献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
5AZV
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Crystal structure of hPPARgamma ligand binding domain complexed with 17-oxoDHA
分子名称: (4~{Z},7~{Z},10~{Z},13~{Z},19~{Z})-17-oxidanylidenedocosa-4,7,10,13,19-pentaenoic acid, Peroxisome proliferator-activated receptor gamma
著者Egawa, D, Itoh, T, Yamamoto, K.
登録日2015-10-23
公開日2016-07-06
最終更新日2020-02-26
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献17-OxoDHA Is a PPAR alpha/gamma Dual Covalent Modifier and Agonist
Acs Chem.Biol., 2016
5AZT
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Ternary complex of hPPARalpha ligand binding domain, 17-oxoDHA and a SRC1 peptide
分子名称: (4~{Z},7~{Z},10~{Z},13~{Z},19~{Z})-17-oxidanylidenedocosa-4,7,10,13,19-pentaenoic acid, 15-meric peptide from Nuclear receptor coactivator 1, Peroxisome proliferator-activated receptor alpha
著者Egawa, D, Itoh, T, Yamamoto, K.
登録日2015-10-23
公開日2016-07-06
最終更新日2020-02-26
実験手法X-RAY DIFFRACTION (3.45 Å)
主引用文献17-OxoDHA Is a PPAR alpha/gamma Dual Covalent Modifier and Agonist
Acs Chem.Biol., 2016
5B41
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Crystal structure of VDR-LBD complexed with 2-methylidene-19-nor-1a,25-dihydroxyvitamin D3
分子名称: (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
著者Anami, Y, Itoh, T, Yamamoto, K.
登録日2016-03-23
公開日2016-12-07
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (1.89 Å)
主引用文献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
7CUC
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Crystal Structure of Urate Oxidase from Bacillus sp. TB-90 in the absence from Chloride Anion at 1.44 A resolution
分子名称: 2-METHOXYETHANOL, 8-AZAXANTHINE, OXYGEN MOLECULE, ...
著者Hibi, T, Itoh, T.
登録日2020-08-22
公開日2020-11-25
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.44 Å)
主引用文献Identification of quasi-stable water molecules near the Thr73-Lys13 catalytic diad of Bacillus sp. TB-90 urate oxidase by X-ray crystallography with controlled humidity.
J.Biochem., 169, 2021
7D9W
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Gamma-glutamyltranspeptidase from Pseudomonas nitroreducens complexed with L-DON
分子名称: 6-DIAZENYL-5-OXO-L-NORLEUCINE, GLYCINE, Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03
著者Hibi, T, Sano, C, Putthapong, P, Hayashi, J, Itoh, T, Wakayama, M.
登録日2020-10-14
公開日2021-06-23
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Mutagenesis and structure-based analysis of the role of Tryptophan525 of gamma-glutamyltranspeptidase from Pseudomonas nitroreducens.
Biochem.Biophys.Res.Commun., 534, 2021
7D9X
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Highly active mutant W525D of Gamma-glutamyltranspeptidase from Pseudomonas nitroreducens
分子名称: GAMMA-BUTYROLACTONE, GLYCEROL, GLYCINE, ...
著者Hibi, T, Sano, C, Itoh, T, Wakayama, M.
登録日2020-10-14
公開日2021-06-23
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.74 Å)
主引用文献Mutagenesis and structure-based analysis of the role of Tryptophan525 of gamma-glutamyltranspeptidase from Pseudomonas nitroreducens.
Biochem.Biophys.Res.Commun., 534, 2021
7D9E
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Gamma-glutamyltranspeptidase from Pseudomonas nitroreducens complexed with L-DON
分子名称: 6-DIAZENYL-5-OXO-L-NORLEUCINE, GLYCEROL, Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03
著者Hibi, T, Sano, C, Itoh, T, Wakayama, M.
登録日2020-10-13
公開日2021-06-23
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.5 Å)
主引用文献Mutagenesis and structure-based analysis of the role of Tryptophan525 of gamma-glutamyltranspeptidase from Pseudomonas nitroreducens.
Biochem.Biophys.Res.Commun., 534, 2021
5XUQ
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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
分子名称: (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
著者Kato, A, Itoh, T, Yamamoto, K.
登録日2017-06-24
公開日2018-06-27
最終更新日2024-03-27
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献Discovery of Potent Vitamin D Receptor Antagonist
To Be Published
5ZJG
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Gamma-glutamyltranspeptidase from Pseudomonas nitroreducens complexed with Gly-Gly
分子名称: GLYCEROL, GLYCINE, Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03 L-subunit, ...
著者Hibi, T, Imaoka, M, Itoh, T, Wakayama, M.
登録日2018-03-20
公開日2019-01-16
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.702 Å)
主引用文献Crystal structure analysis and enzymatic characterization of gamma-glutamyltranspeptidase from Pseudomonas nitroreducens.
Biosci. Biotechnol. Biochem., 83, 2019
5ZWI
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Interaction between Vitamin D receptor (VDR) and a ligand having a dienone group
分子名称: (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
著者Yoshizawa, M, Itoh, T, Anami, Y, Kato, A, Yoshimoto, N, Yamamoto, K.
登録日2018-05-15
公開日2018-07-18
最終更新日2024-03-27
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands
J. Med. Chem., 61, 2018
5ZWH
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Covalent bond formation between histidine of Vitamin D receptor (VDR) and a full agonist having an ene-ynone group via conjugate addition reaction
分子名称: (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, ...
著者Yoshizawa, M, Itoh, T, Anami, Y, Kato, A, Yoshimoto, N, Yamamoto, K.
登録日2018-05-15
公開日2018-07-18
最終更新日2018-08-08
実験手法X-RAY DIFFRACTION (2.38 Å)
主引用文献Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands
J. Med. Chem., 61, 2018
6A6S
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Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans in complex with FSA, Seleno-methionine Derivative
分子名称: (4S,5S)-1,2-DITHIANE-4,5-DIOL, 1-S-(carboxymethyl)-1-thio-beta-D-fructopyranose, FLAVIN-ADENINE DINUCLEOTIDE, ...
著者Ogawa, N, Maruyama, Y, Itoh, T, Hashimoto, W, Murata, K.
登録日2018-06-29
公開日2019-05-15
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.851 Å)
主引用文献Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis.
Sci Rep, 9, 2019
6A6U
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Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with R61G mutation, in complex with FSA
分子名称: (4S,5S)-1,2-DITHIANE-4,5-DIOL, 1-S-(carboxymethyl)-1-thio-beta-D-fructopyranose, FLAVIN-ADENINE DINUCLEOTIDE, ...
著者Ogawa, N, Maruyama, Y, Itoh, T, Hashimoto, W, Murata, K.
登録日2018-06-29
公開日2019-05-15
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.945 Å)
主引用文献Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis.
Sci Rep, 9, 2019
5ZWE
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Covalent bond formation between histidine of Vitamin D receptor (VDR) and a full agonist having a vinyl ketone group via conjugate addition reaction
分子名称: (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
著者Yoshizawa, M, Itoh, T, Anami, Y, Kato, A, Yoshimoto, N, Yamamoto, K.
登録日2018-05-15
公開日2018-07-18
最終更新日2018-08-08
実験手法X-RAY DIFFRACTION (2.72 Å)
主引用文献Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands
J. Med. Chem., 61, 2018
6A6T
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Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with R61G mutation
分子名称: (4S,5S)-1,2-DITHIANE-4,5-DIOL, FLAVIN-ADENINE DINUCLEOTIDE, Fructosyl amine: oxygen oxidoreductase, ...
著者Ogawa, N, Maruyama, Y, Itoh, T, Hashimoto, W, Murata, K.
登録日2018-06-29
公開日2019-05-15
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.901 Å)
主引用文献Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis.
Sci Rep, 9, 2019
6A6V
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Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with 7 additional mutations, in complex with FSA
分子名称: 1-S-(carboxymethyl)-1-thio-beta-D-fructopyranose, FLAVIN-ADENINE DINUCLEOTIDE, Fructosyl amine: oxygen oxidoreductase
著者Ogawa, N, Maruyama, Y, Itoh, T, Hashimoto, W, Murata, K.
登録日2018-06-29
公開日2019-05-15
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.9 Å)
主引用文献Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis.
Sci Rep, 9, 2019
6A6R
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BU of 6a6r by Molmil
Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans, Seleno-methionine Derivative
分子名称: (4S,5S)-1,2-DITHIANE-4,5-DIOL, FLAVIN-ADENINE DINUCLEOTIDE, Fructosyl amine: oxygen oxidoreductase, ...
著者Ogawa, N, Maruyama, Y, Itoh, T, Hashimoto, W, Murata, K.
登録日2018-06-29
公開日2019-05-15
実験手法X-RAY DIFFRACTION (2.609 Å)
主引用文献Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis.
Sci Rep, 9, 2019
5ZWF
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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
分子名称: (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
著者Yoshizawa, M, Itoh, T, Anami, Y, Kato, A, Yoshimoto, N, Yamamoto, K.
登録日2018-05-15
公開日2018-07-18
最終更新日2018-08-08
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands
J. Med. Chem., 61, 2018
5B5B
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Crystal structure of VDR-LBD complexed with 2-methylidene-26,27-diphenyl-19-nor-1,25-dihydroxyvitamin D3
分子名称: (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
著者Kato, A, Itoh, T, Yamamoto, K.
登録日2016-05-02
公開日2016-06-29
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Helix12-Stabilization Antagonist of Vitamin D Receptor
Bioconjug.Chem., 27, 2016
7E2O
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X-ray Crystal structure of PPARgamma R288H mutant.
分子名称: Peroxisome proliferator-activated receptor gamma
著者Egawa, D, Itoh, T.
登録日2021-02-06
公開日2022-01-19
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献Structural Insights into the Loss-of-Function R288H Mutant of Human PPAR gamma.
Biol.Pharm.Bull., 44, 2021
5WQX
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Covalent bond formation of synthetic ligand with hPPARg-LBD
分子名称: 2-[E-(E-2-oxidanylidenehexadec-5-enylidene)amino]ethanoic acid, Peroxisome proliferator-activated receptor gamma
著者Kojima, H, Itoh, T, Yamamoto, K.
登録日2016-11-29
公開日2017-11-22
最終更新日2017-12-13
実験手法X-RAY DIFFRACTION (2.29 Å)
主引用文献On-site reaction for PPAR gamma modification using a specific bifunctional ligand
Bioorg. Med. Chem., 25, 2017
5WR0
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Huisgen cycloaddition for PPARg-LBD labeling by soaking method
分子名称: (E)-N-[(3E)-2-oxo-16-(8-{6-[(trifluoroacetyl)amino]hexanoyl}-8,9-dihydro-1H-dibenzo[b,f][1,2,3]triazolo[4,5-d]azocin-1-yl)hexadec-3-en-1-ylidene]glycine, Peroxisome proliferator-activated receptor gamma
著者Kojima, H, Itoh, T, Yamamoto, K.
登録日2016-11-29
公開日2017-11-22
最終更新日2017-12-13
実験手法X-RAY DIFFRACTION (2.85 Å)
主引用文献On-site reaction for PPAR gamma modification using a specific bifunctional ligand
Bioorg. Med. Chem., 25, 2017

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