Crystal structure of diclofenac bound to the cyclooxygenase active site of COX-2

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 8% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
• DIF · 2-[2,6-dichlorophenyl)amino]benzeneacetic acid · ligand · 4 copies · chains A, B, C, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B, C, D
• BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A, D

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

Pockets

19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• C–D · 2563 Ų buried · 50 hydrogen bonds · protein-protein
• A–B · 2548 Ų buried · 49 hydrogen bonds · protein-protein
• A–C · 416 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide, 12 glycan (disulfide, N-glycosylation).

Compared structures

• 1PXX · Crystal structure of diclofenac bound to the cyclooxygenase active site of COX-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 1PXX · PDBe 1PXX · UniProt Q05769