3WC6
 
 | | Carboxypeptidase B in complex with 2nd zinc | | Descriptor: | ACETATE ION, Carboxypeptidase B, ZINC ION | | Authors: | Yoshimoto, N, Itoh, T, Inaba, Y, Yamamoto, K. | | Deposit date: | 2013-05-24 | | Release date: | 2013-10-02 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Structural basis for inhibition of carboxypeptidase B by selenium-containing inhibitor: selenium coordinates to zinc in enzyme.
J.Med.Chem., 56, 2013
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3VRU
 | | VDR ligand binding domain in complex with 2-Methylidene-19,24-dinor-1alpha,25-dihydroxy vitaminD3 | | Descriptor: | (1R,3R,7E,17beta)-17-[(2R)-5-hydroxy-5-methylhexan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Yoshimoto, N, Inaba, Y, Itoh, T, Nakabayashi, M, Ito, N, Yamamoto, K. | | Deposit date: | 2012-04-14 | | Release date: | 2012-05-23 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands
J.Med.Chem., 55, 2012
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3VRV
 | | VDR ligand binding domain in complex with 2-Methylidene-26,27-dimethyl-19,24-dinor-1alpha,25-dihydroxyvitamin D3 | | Descriptor: | (1R,3R,7E,17beta)-17-[(2R)-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Yoshimoto, N, Inaba, Y, Itoh, T, Nakabayashi, M, Ito, N, Yamamoto, K. | | Deposit date: | 2012-04-14 | | Release date: | 2012-05-23 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands
J.Med.Chem., 55, 2012
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3VRW
 | | VDR ligand binding domain in complex with 22S-Butyl-2-methylidene-26,27-dimethyl-19,24-dinor-1alpha,25-dihydroxyvitamin D3 | | Descriptor: | (1R,3R,7E,17beta)-17-[(2R,3S)-3-butyl-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Yoshimoto, N, Inaba, Y, Itoh, T, Nakabayashi, M, Ito, N, Yamamoto, K. | | Deposit date: | 2012-04-16 | | Release date: | 2012-05-23 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands
J.Med.Chem., 55, 2012
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3WC5
 | | Carboxypeptidase B in complex with DD9 | | Descriptor: | (2R)-7-amino-2-(selanylmethyl)heptanoic acid, CACODYLATE ION, Carboxypeptidase B, ... | | Authors: | Yoshimoto, N, Itoh, T, Inaba, Y, Yamamoto, K. | | Deposit date: | 2013-05-24 | | Release date: | 2013-10-02 | | Last modified: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Structural basis for inhibition of carboxypeptidase B by selenium-containing inhibitor: selenium coordinates to zinc in enzyme.
J.Med.Chem., 56, 2013
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3WC7
 | | Carboxypeptidase B in complex with EF6265 | | Descriptor: | (2S)-7-amino-2-{[(R)-hydroxy{(1R)-2-methyl-1-[(3-phenylpropanoyl)amino]propyl}phosphoryl]methyl}heptanoic acid, Carboxypeptidase B, ZINC ION | | Authors: | Yoshimoto, N, Itoh, T, Inaba, Y, Yamamoto, K. | | Deposit date: | 2013-05-24 | | Release date: | 2013-10-02 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structural basis for inhibition of carboxypeptidase B by selenium-containing inhibitor: selenium coordinates to zinc in enzyme.
J.Med.Chem., 56, 2013
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3WAB
 | | Carboxypeptidase B in complex with DD2 | | Descriptor: | (2R)-7-amino-2-(sulfanylmethyl)heptanoic acid, CACODYLATE ION, Carboxypeptidase B, ... | | Authors: | Yoshimoto, N, Itoh, T, Inaba, Y, Yamamoto, K. | | Deposit date: | 2013-05-01 | | Release date: | 2013-10-02 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.154 Å) | | Cite: | Structural basis for inhibition of carboxypeptidase B by selenium-containing inhibitor: selenium coordinates to zinc in enzyme.
J.Med.Chem., 56, 2013
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3VRT
 | | VDR ligand binding domain in complex with 2-Mehylidene-19,25,26,27-tetranor-1alpha,24-dihydroxyvitaminD3 | | Descriptor: | (1R,3R,7E,17beta)-17-[(2R)-5-hydroxypentan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Nakabayashi, M, Yoshimoto, N, Inaba, Y, Itoh, T, Ito, N, Yamamoto, K. | | Deposit date: | 2012-04-14 | | Release date: | 2012-05-23 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands
J.Med.Chem., 55, 2012
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5ZQQ
 | | Tankyrase-2 in complex with compound 52 | | Descriptor: | 1-methyl-1'-(4-oxo-3,4,5,6,7,8-hexahydroquinazolin-2-yl)spiro[indole-3,4'-piperidin]-2(1H)-one, GLYCEROL, PHOSPHATE ION, ... | | Authors: | Niwa, H, Shirai, F, Sato, S, Yoshimoto, N, Tsumura, T, Okue, M, Shirouzu, M, Seimiya, H, Umehara, T. | | Deposit date: | 2018-04-19 | | Release date: | 2019-04-03 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.29 Å) | | Cite: | Discovery of Novel Spiroindoline Derivatives as Selective Tankyrase Inhibitors.
J. Med. Chem., 62, 2019
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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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5ZQO
 | | Tankyrase-2 in complex with compound 1a | | Descriptor: | 2-[4-(2-methoxyphenyl)piperazin-1-yl]-5,6,7,8-tetrahydroquinazolin-4(3H)-one, GLYCEROL, SULFATE ION, ... | | Authors: | Niwa, H, Shirai, F, Sato, S, Yoshimoto, N, Tsumura, T, Okue, M, Shirouzu, M, Seimiya, H, Umehara, T. | | Deposit date: | 2018-04-19 | | Release date: | 2019-04-03 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.06 Å) | | Cite: | Discovery of Novel Spiroindoline Derivatives as Selective Tankyrase Inhibitors.
J. Med. Chem., 62, 2019
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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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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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5ZQP
 | | Tankyrase-2 in complex with compound 12 | | Descriptor: | 1'-(4-oxo-3,4,5,6,7,8-hexahydroquinazolin-2-yl)-2H-spiro[1-benzofuran-3,4'-piperidin]-2-one, GLYCEROL, PHOSPHATE ION, ... | | Authors: | Niwa, H, Shirai, F, Sato, S, Yoshimoto, N, Tsumura, T, Okue, M, Shirouzu, M, Seimiya, H, Umehara, T. | | Deposit date: | 2018-04-19 | | Release date: | 2019-04-03 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.99 Å) | | Cite: | Discovery of Novel Spiroindoline Derivatives as Selective Tankyrase Inhibitors.
J. Med. Chem., 62, 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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5ZQR
 | | Tankyrase-2 in complex with compound 40c | | Descriptor: | 2-[4,6-difluoro-1-(2-hydroxyethyl)-1,2-dihydro-1'H-spiro[indole-3,4'-piperidin]-1'-yl]-5,6,7,8-tetrahydroquinazolin-4(3H)-one, GLYCEROL, PHOSPHATE ION, ... | | Authors: | Niwa, H, Shirai, F, Sato, S, Yoshimoto, N, Tsumura, T, Okue, M, Shirouzu, M, Seimiya, H, Umehara, T. | | Deposit date: | 2018-04-19 | | Release date: | 2019-04-03 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Discovery of Novel Spiroindoline Derivatives as Selective Tankyrase Inhibitors.
J. Med. Chem., 62, 2019
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6A84
 | | Tankyrase-2 in complex with compound 15d | | Descriptor: | 2-(4-chloro-1,2-dihydro-1'H-spiro[indole-3,4'-piperidin]-1'-yl)-5,6,7,8-tetrahydroquinazolin-4(3H)-one, GLYCEROL, PHOSPHATE ION, ... | | Authors: | Niwa, H, Shirai, F, Sato, S, Yoshimoto, N, Tsumura, T, Okue, M, Shirouzu, M, Seimiya, H, Umehara, T. | | Deposit date: | 2018-07-06 | | Release date: | 2019-04-03 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.98 Å) | | Cite: | Discovery of Novel Spiroindoline Derivatives as Selective Tankyrase Inhibitors.
J. Med. Chem., 62, 2019
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5ZEQ
 | | Carboxypeptidase B in complex with DD28 | | Descriptor: | (2~{S})-2-[(6-azanyl-5-chloranyl-pyridin-3-yl)methyl]-3-selanyl-propanoic acid, CACODYLATE ION, Carboxypeptidase B, ... | | Authors: | Itoh, T, Yoshimoto, N, Yamamoto, K. | | Deposit date: | 2018-02-27 | | Release date: | 2018-06-20 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structural basis for the selective inhibition of activated thrombin-activatable fibrinolysis inhibitor (TAFIa) by a selenium-containing inhibitor with chloro-aminopyridine as a basic group
Bioorg. Med. Chem. Lett., 28, 2018
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2ZMH
 | | Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism | | Descriptor: | (1R,3R,7E,17beta)-17-{(1R,2E,4R)-4-hydroxy-1-methyl-4-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]but-2-en-1-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Nakabayashi, M, Yamada, S, Tanaka, T, Igarashi, M, Yoshimoto, N, Ikura, T, Ito, N, Makishima, M, Tokiwa, H, DeLuca, H.F, Shimizu, M. | | Deposit date: | 2008-04-18 | | Release date: | 2008-09-02 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal structures of rat vitamin d receptor bound to adamantyl vitamin d analogs: structural basis for vitamin d receptor antagonism and partial agonism
J.Med.Chem., 51, 2008
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2ZMJ
 | | Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism | | Descriptor: | (1R,3R,7E,17beta)-17-{(1S,2E,5R)-5-hydroxy-1-methyl-6-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hex-2-en-1-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Nakabayashi, M, Yamada, S, Tanaka, T, Igarashi, M, Yoshimoto, N, Ikura, T, Ito, N, Makishima, M, Tokiwa, H, DeLuca, H.F, Shimizu, M. | | Deposit date: | 2008-04-19 | | Release date: | 2008-09-02 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Crystal structures of rat vitamin d receptor bound to adamantyl vitamin d analogs: structural basis for vitamin d receptor antagonism and partial agonism
J.Med.Chem., 51, 2008
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2ZMI
 | | Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism | | Descriptor: | (1R,3R,7E,17beta)-17-{(1S,2E,5R)-5-hydroxy-1-methyl-5-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]pent-2-en-1-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, 1,2-ETHANEDIOL, FORMIC ACID, ... | | Authors: | Nakabayashi, M, Yamada, S, Tanaka, T, Igarashi, M, Yoshimoto, N, Ikura, T, Ito, N, Makishima, M, Tokiwa, H, DeLuca, H.F, Shimizu, M. | | Deposit date: | 2008-04-19 | | Release date: | 2008-09-02 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Crystal structures of rat vitamin d receptor bound to adamantyl vitamin d analogs: structural basis for vitamin d receptor antagonism and partial agonism
J.Med.Chem., 51, 2008
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3AFR
 | | Crystal Structure of VDR-LBD/22S-Butyl-1a,24R-dihydroxyvitamin D3 complex | | Descriptor: | (1R,3S,5Z)-5-[(2E)-2-{(1R,3aS,7aR)-1-[(1R,2S,4R)-2-butyl-4-hydroxy-1,5-dimethylhexyl]-7a-methyloctahydro-4H-inden-4-yli dene}ethylidene]-4-methylidenecyclohexane-1,3-diol, 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Inaba, Y, Nakabayashi, M, Itoh, T, Ikura, T, Ito, N, Yamamoto, K. | | Deposit date: | 2010-03-10 | | Release date: | 2010-03-31 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | 22S-Butyl-1alpha,24R-dihydroxyvitamin D(3): Recovery of vitamin D receptor agonistic activity
J.Steroid Biochem.Mol.Biol., 121, 2010
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2ZXN
 | | A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket | | Descriptor: | (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2S,3S)-3-(2-hydroxyethyl)heptan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Nakabayashi, M, Ikura, T, Ito, N. | | Deposit date: | 2009-01-04 | | Release date: | 2009-02-17 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | A New Class of Vitamin D Analogues that Induce Structural Rearrangement of the Ligand-Binding Pocket of the Receptor
J.Med.Chem., 52, 2009
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3WT7
 | | Crystal structure of VDR-LBD complexed with 22R-Butyl-2-methylidene-26,27-dimethyl-19,24-dinor-1 ,25-dihydroxyvitamin D3 | | Descriptor: | (1R,3R,7E,17beta)-17-[(2R,3R)-3-butyl-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Anami, Y, Itoh, T, Yamamoto, K. | | Deposit date: | 2014-04-08 | | Release date: | 2014-06-11 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | A Mixed Population of Antagonist and Agonist Binding Conformers in a Single Crystal Explains Partial Agonism against Vitamin D Receptor: Active Vitamin D Analogues with 22R-Alkyl Group.
J.Med.Chem., 57, 2014
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3WT6
 | | A mixed population of antagonist and agonist binding conformers in a single crystal explains partial agonism against vitamin D receptor: Active vitamin D analogues with 22R-alkyl group | | Descriptor: | (1R,3R,7E,17beta)-17-[(2R,3R)-3-butyl-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Anami, Y, Itoh, T, Yamamoto, K. | | Deposit date: | 2014-04-08 | | Release date: | 2014-06-11 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | A Mixed Population of Antagonist and Agonist Binding Conformers in a Single Crystal Explains Partial Agonism against Vitamin D Receptor: Active Vitamin D Analogues with 22R-Alkyl Group.
J.Med.Chem., 57, 2014
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