Crystal structure of T. brucei pde-B1 catalytic domain with inhibitor npd-055

Structure

x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).

Ligands and binding sites

• GAI · Guanidine · ligand · 5 copies · chains A, B
• K3N · 3-[5-[(4~{a}~{R},8~{a}~{S})-3-cycloheptyl-4-oxidanylidene-4~{a},5,6,7,8,8~{a}-hexahydrophthalazin-1-yl]-2-methoxy-phenyl]-~{N}-butyl-prop-2-ynamide · ligand · 2 copies · chains A, B
• ZN · Zinc ion · metal · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B
• GOL · Glycerol · additive · 3 copies · chains A, B
• FMT · Formic acid · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 712 Ų buried · 3 hydrogen bonds · protein-protein

Compared structures

• 6RGK · Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-055 · the same entry in another collection · 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 Q8WQX9
• Elsewhere: RCSB PDB 6RGK · PDBe 6RGK · UniProt Q8WQX9