The complex of murine cyclooxygenase-2 with a conjugate of indomefathin and podophyllotoxin, N-{(SUCCINYLPODOPHYLLOTOXINYL)BUT- 4-yl}-2-{1-(4-chlorobenzoyl)-5-methoxy-2-methyl-1H-indol-3- YL}ACETAMIDE

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 9% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
• IXP · (5S,5aS,8aS,9S)-8-oxo-9-(3,4,5-trimethoxyphenyl)-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol-5-yl 4-{[4-({[1-(4-chlorobenzoyl)-5-methoxy-2-methyl-1H-indol-3-yl]acetyl}amino)butyl]amino}-4-oxobutanoate · ligand · 4 copies · chains A, B, C, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
• BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains B, D

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 2648 Ų buried · 52 hydrogen bonds · protein-protein
• C–D · 2636 Ų buried · 52 hydrogen bonds · protein-protein
• B–C · 427 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide, 12 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).

Compared structures

• 4OTJ · The complex of murine cyclooxygenase-2 with a conjugate of indomefathin and… · 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 4OTJ · PDBe 4OTJ · UniProt Q05769