Structure of ret protein tyrosine kinase domain in complex with nintedanib

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).

Ligands and binding sites

• XIN · Methyl (3Z)-3-{[(4-{methyl[(4-methylpiperazin-1-yl) acetyl]amino}phenyl)amino](phenyl)methylidene}-2-oxo-2,3-dihydro-1H-indole-6-carboxylate · ligand · 2 copies · chains A, C
• FMT · Formic acid · additive · 2 copies · chains A, C

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–C · 1457 Ų buried · 14 hydrogen bonds · protein-protein

Compared structures

• 6NEC · Structure of ret protein tyrosine kinase domain in complex with nintedanib · 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 A against A, TM-score 0.95

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 6NEC · PDBe 6NEC · UniProt P07949