7Z93

Crystal structure of YTHDF2 with compound YLI_DF_022

7Z93 の概要

• エントリーDOI: 10.2210/pdb7z93/pdb
• 分子名称: YTH domain-containing family protein 2, CHLORIDE ION, SULFATE ION, ... (5 entities in total)
• 機能のキーワード: epitranscriptomic reader, m6a reader, rna binding protein
• 由来する生物種: Homo sapiens (human)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 39693.29

構造登録者

Nai, F.,Li, Y.,Caflisch, A. (登録日: 2022-03-19, 公開日: 2022-03-30, 最終更新日: 2024-01-31)

主引用文献

Nai, F.,Nachawati, R.,Zalesak, F.,Wang, X.,Li, Y.,Caflisch, A.
Fragment Ligands of the m 6 A-RNA Reader YTHDF2.
Acs Med.Chem.Lett., 13:1500-1509, 2022

PubMed Abstract: We report 17 small-molecule ligands that compete with -methyladenosine (mA) for binding to the mA-reader domain of YTHDF2 (YT521-B homology domain family 2). We determined their binding mode at high resolution by X-ray crystallography and quantified their affinity by a fluorescence-based binding assay. 6-Cyclopropyluracil and a pyrazolopyrimidine derivative have favorable ligand efficiencies of 0.47 and 0.38 kcal mol per non-hydrogen atom, respectively. They represent useful starting points for hit optimization.

PubMed: 36110386
DOI: 10.1021/acsmedchemlett.2c00303

実験手法

X-RAY DIFFRACTION (1.97 Å)