7YX6 image
Deposition Date 2022-02-15
Release Date 2022-02-23
Last Version Date 2024-01-31
Entry Detail
PDB ID:
7YX6
Keywords:
RNA BINDING PROTEIN
Title:
Crystal structure of YTHDF2 with compound YLI_DF_027
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.80 Å
R-Value Free:
0.19
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 65
7YX6 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:YTH domain-containing family protein 2
Gene (Uniprot):YTHDF2
Chain IDs:A, B
Chain Length:167
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:Q9Y5A9 Pfam ID:PF04146
Ligand Molecules
GOL
I6R
SO4
Primary Citation
Fragment Ligands of the m 6 A-RNA Reader YTHDF2.
Acs Med.Chem.Lett. 13 1500 1509 (2022)
PMID: 36110386 DOI: 10.1021/acsmedchemlett.2c00303

Abstact

We report 17 small-molecule ligands that compete with N6-methyladenosine (m6A) for binding to the m6A-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-1 per non-hydrogen atom, respectively. They represent useful starting points for hit optimization.

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Disease

Primary Citation of related structures
7YX6