Crystal structure of partially phosphorylated ret V804M tyrosine kinase domain complexed with PDD00018412

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).

Ligands and binding sites

• H6W · ~{N}-[3-(1,3-benzodioxol-5-yl)pyrazolo[1,5-a]pyrimidin-5-yl]-~{N}',~{N}'-dimethyl-propane-1,3-diamine · ligand · 2 copies · chains A, B
• CL · Chloride ion · ion · chains B
• FMT · Formic acid · additive · 15 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 5 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1398 Ų buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

• 6I82 · Crystal structure of partially phosphorylated RET V804M tyrosine kinase domain complexed… · the same entry in another collection · chain A against A, TM-score 1.00
• P07949 · AlphaFold monomer V2.0 prediction for proto-oncogene tyrosine-protein kinase receptor ret… · 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 P07949
• Elsewhere: RCSB PDB 6I82 · PDBe 6I82 · UniProt P07949