Structure-based evolution of a hybrid steroid series of autotaxin inhibitors

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 19% strand (DSSP).

Ligands and binding sites

• 7C8 · [3,5-bis(chloranyl)phenyl]methyl 4-[(4~{R})-4-[(3~{R}, 5~{S},7~{S},8~{R},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3,7-bis(oxidanyl)-2,3,4,5,6,7,8,9,11, 12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentyl]piperazine-1-carboxylate · ligand · chains A
• MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
• BMA · beta-D-mannopyranose · sugar
• ZN · Zinc ion · metal · 2 copies · chains A
• CA · Calcium ion · metal · chains A
• NA · Sodium ion · metal · chains A
• IOD · Iodide ion · ion · 9 copies · chains A
• SCN · Thiocyanate ion · ion · 4 copies · chains A
• GOL · Glycerol · additive · 3 copies · chains A

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

Pockets

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

Modifications

Observed in the structure: 14 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

• 5M0D · Structure-based evolution of a hybrid steroid series of Autotaxin inhibitors · the same entry in another collection · chain A against A, TM-score 1.00
• Q64610 · 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 Q64610
• Elsewhere: RCSB PDB 5M0D · PDBe 5M0D · UniProt Q64610