Crystal structure of a hydroxamate based inhibitor EN140 in complex with the mmp-9 catalytic domain

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 17% strand (DSSP).

Ligands and binding sites

• E40 · (2R)-4-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)-N-hydroxy-2-{[(4'-methoxybiphenyl-4-yl)sulfonyl](propan-2-yloxy)amino}butanamide · ligand · 2 copies · chains A, B
• NA · Sodium ion · metal · 7 copies · chains B
• CA · Calcium ion · metal · 6 copies · chains A, B
• ZN · Zinc ion · metal · 4 copies · chains A, B
• AZI · Azide ion · ion
• PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
• PGO · S-1,2-propanediol · additive · 2 copies · chains A
• GOL · Glycerol · additive · chains B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 275 Ų buried · 3 hydrogen bonds · protein-protein

Compared structures

• 4WZV · Crystal structure of a hydroxamate based inhibitor EN140 in complex with the MMP-9… · the same entry in another collection · chain A against A, TM-score 1.00
• P14780 · AlphaFold monomer V2.0 prediction for matrix metalloproteinase-9 (P14780) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P14780
• Elsewhere: RCSB PDB 4WZV · PDBe 4WZV · UniProt P14780