The structure of vioxx bound to human COX-2

Structure

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

Ligands and binding sites

• RCX · Rofecoxib · ligand · 2 copies · chains A, B
• COH · Protoporphyrin IX containing co · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
• MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
• PO4 · Phosphate ion · ion · 6 copies · chains A, B
• NH4 · Ammonium ion · ion · 2 copies · chains A, B
• GOL · Glycerol · additive · 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, 5 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 2485 Ų buried · 43 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 5 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand, glycosylation).

Compared structures

• 5KIR · The Structure of Vioxx Bound to Human COX-2 · the same entry in another collection · chain A against A, TM-score 1.00
• P35354 · AlphaFold monomer V2.0 prediction for prostaglandin G/H synthase 2 (P35354) · 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 P35354
• Elsewhere: RCSB PDB 5KIR · PDBe 5KIR · UniProt P35354