Crystal structure of mouse autotaxin in complex with compound 1A

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 20% strand (DSSP).

Ligands and binding sites

• O9W · (~{E})-3-[4-chloranyl-2-[(5-methyl-1,2,3,4-tetrazol-2-yl)methyl]phenyl]-1-[(2~{R})-4-[(4-fluorophenyl) methyl]-2-methyl-piperazin-1-yl]prop-2-en-1-one · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
• MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
• BMA · beta-D-mannopyranose · sugar
• NA · Sodium ion · metal · 4 copies · chains A
• ZN · Zinc ion · metal · 2 copies · chains A
• CL · Chloride ion · ion · 2 copies · chains A
• PO4 · Phosphate ion · ion · chains A

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

Pockets

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

Modifications

Observed in the structure: 15 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

• 6Y5M · Crystal structure of mouse Autotaxin in complex with compound 1a · the same entry in another collection · chain A against A, TM-score 1.00
• Q9R1E6 · AlphaFold monomer V2.0 prediction for ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE… · a predicted model of the same protein · chain A against A, TM-score 1.00

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 Q9R1E6
• Elsewhere: RCSB PDB 6Y5M · PDBe 6Y5M · UniProt Q9R1E6