Leishmania mexicana cpb in complex with an aza-nitrile inhibitor

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 24% strand (DSSP).

Ligands and binding sites

• GES · 3-tert-butyl-N-[(2S)-1-(2-cyano-1,2-dimethylhydrazinyl)-4-methyl-1-oxopentan-2-yl]-1-methyl-1H-pyrazole-5-carboxamide (non-preferred name) · ligand · 2 copies · chains A, B
• NA · Sodium ion · metal · 2 copies · chains A, B
• ACT · Acetate ion · additive · 6 copies · chains A, B
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 845 Ų buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

• 6P4E · Leishmania mexicana CPB in complex with an aza-nitrile inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
• P36400 · AlphaFold monomer V2.0 prediction for cysteine proteinase B (P36400) · a predicted model of the same protein · chain A 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 P36400
• Elsewhere: RCSB PDB 6P4E · PDBe 6P4E · UniProt P36400