Sodium in PDB 8bpy: X-Ray Structure of PDE9A in Complex with Inhibitor 13A

All present enzymatic activity of X-Ray Structure of PDE9A in Complex with Inhibitor 13A:
3.1.4.35;

The structure of X-Ray Structure of PDE9A in Complex with Inhibitor 13A, PDB code: 8bpy was solved by H.Steuber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.74 / 3.30
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	222.423, 222.423, 120.257, 90, 90, 90
R / Rfree (%)	24.6 / 31.2

The structure of X-Ray Structure of PDE9A in Complex with Inhibitor 13A also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Sodium atom in the X-Ray Structure of PDE9A in Complex with Inhibitor 13A (pdb code 8bpy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of PDE9A in Complex with Inhibitor 13A, PDB code: 8bpy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of PDE9A in Complex with Inhibitor 13A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of PDE9A in Complex with Inhibitor 13A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2003 b:30.9 occ:0.00 O A:ASP244 2.3 99.6 1.0 O A:TYR246 2.7 100.0 1.0 C A:ASP244 3.5 90.9 1.0 C A:TYR246 3.8 90.8 1.0 CA A:ASP244 4.3 96.9 1.0 O A:HIS243 4.3 89.7 1.0 CA A:ARG247 4.4 100.3 1.0 N A:ASN245 4.4 86.7 1.0 N A:ARG247 4.5 99.8 1.0 N A:TYR246 4.6 86.9 1.0 CA A:ASN245 4.7 83.7 1.0 C A:ASN245 4.7 83.6 1.0 CA A:TYR246 4.9 80.6 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of PDE9A in Complex with Inhibitor 13A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of PDE9A in Complex with Inhibitor 13A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2003 b:76.9 occ:0.00 O B:ASP244 2.1 167.8 1.0 O B:TYR246 2.2 143.7 1.0 C B:ASP244 3.0 189.2 1.0 C B:TYR246 3.4 153.3 1.0 CA B:ASP244 3.7 182.1 1.0 O B:HIS243 3.8 148.3 1.0 N B:TYR246 3.9 164.2 1.0 N B:ASN245 4.0 200.5 1.0 OD1 B:ASP244 4.1 174.8 1.0 CA B:ASN245 4.3 187.6 1.0 N B:ARG247 4.3 159.3 1.0 CA B:ARG247 4.4 174.1 1.0 CA B:TYR246 4.4 155.6 1.0 C B:ASN245 4.6 166.2 1.0 CG B:ASP244 4.7 190.8 1.0 C B:HIS243 4.7 156.9 1.0 N B:ASP244 4.7 164.5 1.0 CB B:ASP244 4.8 187.8 1.0

D.Meibom, S.Micus, A.L.Andreevski, S.Anlauf, P.Bogner, C.J.Von Buehler, A.P.Dieskau, J.Dreher, F.Eitner, D.Fliegner, M.Follmann, K.M.Gericke, S.Maassen, J.Meyer, K.H.Schlemmer, H.Steuber, A.Tersteegen, F.Wunder. Bay-7081: A Potent, Selective, and Orally Bioavailable Cyanopyridone-Based PDE9A Inhibitor. J.Med.Chem. V. 65 16420 2022.
ISSN: ISSN 0022-2623
PubMed: 36475653
DOI: 10.1021/ACS.JMEDCHEM.2C01267