Structure of DDR1 receptor tyrosine kinase in complex with D2164 inhibitor at 2.65 ångströms resolution.

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).

Ligands and binding sites

• 5X1 · 3-[(4-methylpiperazin-1-yl)methyl]-~{N}-[(4~{R})-4-methyl-2-pyrimidin-5-yl-3,4-dihydro-1~{H}-isoquinolin-7-yl]-5-(trifluoromethyl)benzamide · ligand · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
• PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, A

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 846 Ų buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

• 5FDX · Structure of DDR1 receptor tyrosine kinase in complex with D2164 inhibitor at 2.65… · the same entry in another collection · chain A against A, TM-score 1.00
• Q08345 · AlphaFold monomer V2.0 prediction for epithelial discoidin domain- containing receptor 1… · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q08345
• Elsewhere: RCSB PDB 5FDX · PDBe 5FDX · UniProt Q08345