Crystal structure of an mmp twin carboxylate based inhibitor LC20 in complex with the mmp-9 catalytic domain

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 17% strand (DSSP).

Ligands and binding sites

• 0ZD · N,N'-bis(2-[(biphenyl-4ylsulfonyl)[(2R)-1-hydroxy-3-methyl-1-oxobutan-2-yl]-amino]ethyl)benzene-1,3-dicarboxamide · ligand · chains A, B
• MLT · D-malate · ligand · chains B
• CA · Calcium ion · metal · 6 copies · chains A, B
• ZN · Zinc ion · metal · 4 copies · chains A, B
• PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B
• PGO · S-1,2-propanediol · additive · 6 copies · chains A, B
• GOL · Glycerol · additive · 5 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 195 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 4HMA · Crystal structure of an MMP twin carboxylate based inhibitor LC20 in complex with the… · 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 4HMA · PDBe 4HMA · UniProt P14780