Crystal structure of trka kinase with ligand

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).

Ligands and binding sites

• 7HF · 1-[(3S,4R)-4-[3,4-bis(fluoranyl)phenyl]-1-(2-methoxyethyl)pyrrolidin-3-yl]-3-(5-ethoxy-4-methyl-2-phenyl-pyrazol-3-yl)urea · ligand · chains A
• NA · Sodium ion · metal · chains A
• DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A

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

Pockets

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

Modifications

Observed in the structure: 2 covalent (additive adduct).

Compared structures

• 5H3Q · Crystal Structure of TrkA kinase with ligand · the same entry in another collection · chain A against A, TM-score 1.00
• P04629 · AlphaFold monomer V2.0 prediction for high affinity nerve growth factor receptor (P04629) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P04629
• Elsewhere: RCSB PDB 5H3Q · PDBe 5H3Q · UniProt P04629