New irreversible a-L-iduronidase inhibitors and activity-based probes

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).

Ligands and binding sites

• H6B · (1~{R},2~{R},3~{R},4~{S},5~{S},6~{R})-7-methyl-3,4,5-tris(oxidanyl)-7-azabicyclo[4.1.0]heptane-2-carboxylic acid · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
• MAN · alpha-D-mannopyranose · sugar · 5 copies · chains B, A
• BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
• CL · Chloride ion · ion · 2 copies · chains A, B
• GOL · Glycerol · additive · 9 copies · chains A, B
• TLA · L(+)-tartaric acid · additive · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 244 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

• 6I6X · New Irreversible a-l-Iduronidase Inhibitors and Activity-Based Probes · the same entry in another collection · chain A against A, TM-score 1.00
• P35475 · AlphaFold monomer V2.0 prediction for alpha-L-iduronidase (P35475) · 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 P35475
• Elsewhere: RCSB PDB 6I6X · PDBe 6I6X · UniProt P35475