7Z4U
Crystal structure of YTHDF2 with compound YLI_DF_028
Summary for 7Z4U
Entry DOI | 10.2210/pdb7z4u/pdb |
Descriptor | YTH domain-containing family protein 2, SULFATE ION, CHLORIDE ION, ... (6 entities in total) |
Functional Keywords | epitranscriptomic reader, m6a reader, rna binding protein |
Biological source | Homo sapiens (human) |
Total number of polymer chains | 2 |
Total formula weight | 39579.85 |
Authors | Nai, F.,Li, Y.,Caflisch, A. (deposition date: 2022-03-04, release date: 2022-03-16, Last modification date: 2024-01-31) |
Primary citation | 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 Cited by 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: 36110386DOI: 10.1021/acsmedchemlett.2c00303 PDB entries with the same primary citation |
Experimental method | X-RAY DIFFRACTION (1.83 Å) |
Structure validation
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