Crystal structure of protac MS67 in complex with the wd repeat- containing protein 5 and PVHL:ELONGINC:ELONGINB

Structure

x-ray diffraction · 4 distinct chains · 14% helix, 40% strand (DSSP).

Ligands and binding sites

• X6M · N-(6-fluoro-3'-{[6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carbonyl]amino}-4'-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-carbonyl) glycyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide · ligand · chains L, A
• GOL · Glycerol · additive · chains L, A

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

Pockets

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

Interfaces

4 interfaces between chains.

• J–K · 1133 Ų buried · 13 hydrogen bonds · protein-protein
• K–L · 1032 Ų buried · 10 hydrogen bonds · protein-protein
• L–A · 458 Ų buried · 3 hydrogen bonds · protein-protein
• J–L · 185 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 7JTP · Crystal structure of Protac MS67 in complex with the WD repeat-containing protein 5 and… · the same entry in another collection · chain J against J, TM-score 1.00
• Q15370 · AlphaFold monomer V2.0 prediction for elongin-B (Q15370) · a predicted model of the same protein · chain J against A, TM-score 0.99
• Q15369 · AlphaFold monomer V2.0 prediction for elongin-C (Q15369) · a predicted model of the same protein · chain K 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 Q15370
• Every structure of UniProt Q15369
• Every structure of UniProt P40337
• Every structure of UniProt P61964
• Elsewhere: RCSB PDB 7JTP · PDBe 7JTP · UniProt Q15370 · UniProt Q15369 · UniProt P40337 · UniProt P61964