5B5B

Crystal structure of VDR-LBD complexed with 2-methylidene-26,27-diphenyl-19-nor-1,25-dihydroxyvitamin D3

5B5B の概要

• エントリーDOI: 10.2210/pdb5b5b/pdb
• 分子名称: Vitamin D3 receptor, Mediator of RNA polymerase II transcription subunit 1, (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, ... (4 entities in total)
• 機能のキーワード: transcription, vitamin d3, vdr, vdre, rxr, co-factors, antagonist
• 由来する生物種: Rattus norvegicus (Rat); 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 65469.53

構造登録者

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)

主引用文献

Kato, A.,Itoh, T.,Anami, Y.,Egawa, D.,Yamamoto, K.
Helix12-Stabilization Antagonist of Vitamin D Receptor
Bioconjug.Chem., 27:1750-1761, 2016

PubMed Abstract: To develop strong vitamin D receptor (VDR) antagonists and reveal their antagonistic mechanism, we designed and synthesized vitamin D analogues with bulky side chains based on the "active antagonist" concept in which antagonist prevents helix 12 (H12) folding. Of the synthesized analogues, compounds 3a and 3b showed strong antagonistic activity. Dynamic hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) and static X-ray crystal structure analyses indicated that compound 3a stabilizes H11-H12 but displaces H6-H7 so that 3a is a novel rather than "active" or "passive" type of antagonist. We classified 3a as a third type of antagonist and called it "H11-H12 stabilization antagonist". HDX-MS analysis indicated that antagonist 3b is an "active" antagonist. To date there are no reports relating to nuclear receptor antagonist that strongly stabilizes H12. In this study, we found first VDR antagonist that stabilizes H12 and we showed that antagonistic mechanism is diverse depending on each antagonist structure. Additionally, HDX-MS was proven to be very useful for investigations of protein structure alterations resulting from ligand binding.

PubMed: 27294600
DOI: 10.1021/acs.bioconjchem.6b00246

実験手法

X-RAY DIFFRACTION (2 Å)