Crystal structure of YTHDF2 with compound ZA_166

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 30% strand (DSSP).

Ligands and binding sites

• IFZ · 3-bromanyl-~{N}-methyl-2~{H}-pyrazolo[4,3-d]pyrimidin-7-amine · ligand · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 4 copies · chains A, B
• GOL · Glycerol · additive · 3 copies · chains B, A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 453 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 7Z8P · Crystal structure of YTHDF2 with compound ZA_166 · the same entry in another collection · chain A against A, TM-score 1.00
• Q9Y5A9 · AlphaFold monomer V2.0 prediction for yth domain-containing family protein 2 (Q9Y5A9) · a predicted model of the same protein · chain B against A, TM-score 0.96

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q9Y5A9
• Elsewhere: RCSB PDB 7Z8P · PDBe 7Z8P · UniProt Q9Y5A9