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7Z4U

Crystal structure of YTHDF2 with compound YLI_DF_028

Summary for 7Z4U
Entry DOI10.2210/pdb7z4u/pdb
DescriptorYTH domain-containing family protein 2, SULFATE ION, CHLORIDE ION, ... (6 entities in total)
Functional Keywordsepitranscriptomic reader, m6a reader, rna binding protein
Biological sourceHomo sapiens (human)
Total number of polymer chains2
Total formula weight39579.85
Authors
Nai, F.,Li, Y.,Caflisch, A. (deposition date: 2022-03-04, release date: 2022-03-16, Last modification date: 2024-01-31)
Primary citationNai, 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: 36110386
DOI: 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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