X-ray structure of of human glutamate carboxypeptidase II (gcpii) in a complex with ceibzl, a urea-based inhibitor N~2~-{[(1S)-1-carboxybut- 3-yn-1-YL]CARBAMOYL}-N~6~-(4-iodobenzoyl)-L-lysine

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).

Ligands and binding sites

• 2QQ · N~2~-{[(1S)-1-carboxybut-3-yn-1-yl]carbamoyl}-N~6~-(4-iodobenzoyl)-L-lysine · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A
• FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
• BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
• MAN · alpha-D-mannopyranose · sugar
• ZN · Zinc ion · metal · 2 copies · chains A
• CA · Calcium ion · metal · chains A
• CL · Chloride ion · ion · chains A

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

Pockets

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

Modifications

Observed in the structure: 7 glycan (N-glycosylation).

Compared structures

• 4OC2 · X-ray structure of of human glutamate carboxypeptidase II (GCPII) in a complex with… · the same entry in another collection · chain A against A, TM-score 1.00
• Q04609 · AlphaFold monomer V2.0 prediction for glutamate carboxypeptidase 2 (Q04609) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q04609
• Elsewhere: RCSB PDB 4OC2 · PDBe 4OC2 · UniProt Q04609