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3VRU
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BU of 3vru by Molmil
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
3VRV
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BU of 3vrv by Molmil
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
3VRW
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BU of 3vrw by Molmil
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
3WC7
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BU of 3wc7 by Molmil
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:2023-11-08
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
3WC5
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BU of 3wc5 by Molmil
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:2022-08-24
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
3WC6
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BU of 3wc6 by Molmil
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:2023-11-08
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
3WAB
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BU of 3wab by Molmil
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:2023-11-08
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
3VRT
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BU of 3vrt by Molmil
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
2ZMI
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BU of 2zmi by Molmil
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
2ZMH
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BU of 2zmh by Molmil
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
2ZMJ
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BU of 2zmj by Molmil
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
5ZEQ
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BU of 5zeq by Molmil
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:2018-07-04
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
5ZQQ
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BU of 5zqq by Molmil
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
5ZWI
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BU of 5zwi by Molmil
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
5ZQO
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BU of 5zqo by Molmil
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
5ZWH
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BU of 5zwh by Molmil
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:2018-08-08
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
5ZWF
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BU of 5zwf by Molmil
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
5ZQP
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BU of 5zqp by Molmil
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
5ZWE
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BU of 5zwe by Molmil
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
5ZQR
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BU of 5zqr by Molmil
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
6A84
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BU of 6a84 by Molmil
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
2ZXM
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BU of 2zxm by Molmil
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-[(2R,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 (3.01 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
3AFR
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BU of 3afr by Molmil
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
2ZXN
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BU of 2zxn by Molmil
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
3WT5
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BU of 3wt5 by Molmil
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 (1.9 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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