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PDB: 143 results

5AWK
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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
5AWJ
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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
5AZV
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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
5B41
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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
5B5B
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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
7E2O
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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
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
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
2E9Q
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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
7EFQ
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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
5ZWI
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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
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
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
5ZJG
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BU of 5zjg by Molmil
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
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
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
6A6U
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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
6A6T
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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
6A6V
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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
6A6R
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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
6A6S
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BU of 6a6s by Molmil
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
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
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
5XPL
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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
5XPM
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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
5XPN
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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
5XPP
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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
5XPO
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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
3VQU
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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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