X-ray crystal structure of ns-398 bound to the cyclooxygenase channel of cyclooxygenase-2

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 9% strand (DSSP).

Ligands and binding sites

• NS4 · N-[2-(cyclohexyloxy)-4-nitrophenyl]methanesulfonamide · ligand · 2 copies · chains A, B
• HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
• NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies
• BMA · beta-D-mannopyranose · sugar
• MAN · alpha-D-mannopyranose · sugar · chains B
• GOL · Glycerol · additive · 6 copies · chains A, B
• BOG · octyl beta-D-glucopyranoside · additive · chains A

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

Pockets

7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 2622 Ų buried · 40 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

• 3QMO · X-ray crystal structure of NS-398 bound to the cyclooxygenase channel of cyclooxygenase-2 · the same entry in another collection · chain A against A, TM-score 1.00
• Q05769 · AlphaFold monomer V2.0 prediction for prostaglandin G/H synthase 2 (Q05769) · 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 Q05769
• Elsewhere: RCSB PDB 3QMO · PDBe 3QMO · UniProt Q05769