Crystal structure of PDE5 in complex with sildenafil

Structure

x-ray diffraction · resolution 2.3 · 2 distinct chains · 70% helix, 0% strand (DSSP).

Ligands and binding sites

• VIA · 5-{2-ethoxy-5-[(4-methylpiperazin-1-yl)sulfonyl]phenyl}-1-methyl-3-propyl-1H,6H,7H-pyrazolo[4,3-d]pyrimidin-7-one · ligand · 3 copies · chains A, B, C
• ZN · Zinc ion · metal · 3 copies · chains A, B, C
• MG · Magnesium ion · metal · 3 copies · chains A, B, C

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

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 788 Ų buried · 17 hydrogen bonds · protein-protein
• B–C · 500 Ų buried · 6 hydrogen bonds · protein-protein
• A–C · 443 Ų buried · 7 hydrogen bonds · protein-protein

Compared structures

• 2H42 · Crystal structure of PDE5 in complex with sildenafil · the same entry in another collection · chain A against A, TM-score 1.00
• O76074 · AlphaFold monomer V2.0 prediction for cgmp-specific 3',5'-cyclic phosphodiesterase… · a predicted model of the same protein · chain B against A, TM-score 0.97

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 O76074
• Elsewhere: RCSB PDB 2H42 · PDBe 2H42 · UniProt O76074