Crystal structure of T. brucei pde-B1 catalytic domain with inhibitor npd-001

Structure

x-ray diffraction · 2 distinct chains · 73% helix, 0% strand (DSSP).

Ligands and binding sites

• GAI · Guanidine · ligand · 7 copies · chains A, B
• 6M5 · (4~{A}~{S},8~{A}~{R})-2-cycloheptyl-4-[4-methoxy-3-[4-[4-(1~{H}-1,2,3,4-tetrazol-5-yl) phenoxy]butoxy]phenyl]-4~{A},5,8,8~{A}-tetrahydrophthalazin-1-one · 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 · 8 copies · chains A, B
• FMT · Formic acid · additive · 2 copies · chains A
• PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 746 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 5G57 · Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-001 · 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 5G57 · PDBe 5G57 · UniProt Q8WQX9