Crystal structure of the PDE9A catalytic domain in complex with inhibitor 28

Structure

x-ray diffraction · 1 distinct chain · 69% helix, 0% strand (DSSP).

Ligands and binding sites

• LUO · N-(4-methoxyphenyl)-N~2~-[1-(2-methylphenyl)-4-oxo-4,5-dihydro-1H-pyrazolo[3,4-d]pyrimidin-6-yl]-L-alaninamide · ligand · 3 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, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1042 Ų buried · 10 hydrogen bonds · protein-protein

Compared structures

• 4GH6 · Crystal structure of the PDE9A catalytic domain in complex with inhibitor 28 · 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 0.98

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 4GH6 · PDBe 4GH6 · UniProt O76083