Crystal structure of the PDE9 catalytic domain in complex with inhibitor 2

Structure

x-ray diffraction · 1 distinct chain · 73% helix, 0% strand (DSSP).

Ligands and binding sites

• 9Q9 · 1-cyclopentyl-6-({(2R)-1-[(3S)-3-fluoropyrrolidin-1-yl]-1-oxopropan-2-yl}amino)-1,5-dihydro-4H-pyrazolo[3, 4-d]pyrimidin-4-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

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 · 858 Ų buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

• 6A3N · Crystal structure of the PDE9 catalytic domain in complex with inhibitor 2 · the same entry in another collection · chain A against A, TM-score 1.00
• O76083 · AlphaFold monomer V2.0 prediction for high affinity cgmp-specific 3',5'-cyclic… · 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 O76083
• Elsewhere: RCSB PDB 6A3N · PDBe 6A3N · UniProt O76083