Crystal structure of T. brucei pde-B1 catalytic domain with inhibitor npd-039

Structure

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

Ligands and binding sites

• 908 · 4-[5-[(4~{A}~{R},8~{A}~{S})-4-oxidanylidene-3-propan-2-yl-4~{A},5,8,8~{A}-tetrahydrophthalazin-1-yl]-2-methoxy-phenyl]-~{N}-(2-azanyl-2-oxidanylidene-ethyl) benzamide · ligand · 2 copies · chains A, B
• GAI · Guanidine · ligand · chains A
• ZN · Zinc ion · metal · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B
• FMT · Formic acid · additive · 4 copies · chains A, B
• GOL · Glycerol · additive · 3 copies · chains A, B
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 697 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

• 5L8C · Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-039 · 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 5L8C · PDBe 5L8C · UniProt Q8WQX9