Zinc 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:

Magnesium	(Mg)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of PDE9A in Complex with Inhibitor 13A, PDB code: 8bpy:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn2001 b:17.1 occ:0.00 OD1 A:ASP293 1.7 41.9 1.0 NE2 A:HIS292 1.9 79.3 1.0 OD2 A:ASP402 2.3 75.8 1.0 NE2 A:HIS256 2.4 78.7 1.0 CG A:ASP293 2.5 63.5 1.0 CD2 A:HIS256 2.7 93.8 1.0 CE1 A:HIS292 2.9 90.6 1.0 CD2 A:HIS292 2.9 83.8 1.0 OD2 A:ASP293 3.0 55.0 1.0 CG A:ASP402 3.4 72.2 1.0 CB A:ASP293 3.5 67.1 1.0 CE1 A:HIS256 3.6 91.0 1.0 MG A:MG2002 3.9 13.8 0.0 CG A:HIS256 4.0 92.7 1.0 OD1 A:ASP402 4.0 51.7 1.0 ND1 A:HIS292 4.0 83.2 1.0 CD2 A:HIS252 4.0 109.9 1.0 CG A:HIS292 4.1 81.9 1.0 NE2 A:HIS252 4.1 115.2 1.0 O A:ASP402 4.1 106.3 1.0 ND1 A:HIS256 4.4 92.5 1.0 CG2 A:VAL260 4.6 72.0 1.0 CB A:ASP402 4.6 68.8 1.0 CA A:ASP402 4.6 75.0 1.0 CA A:ASP293 4.8 76.6 1.0 C A:ASP402 4.8 91.2 1.0 N A:ASP293 5.0 82.8 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn2001 b:63.1 occ:0.00 OD1 B:ASP402 1.4 82.3 1.0 OD2 B:ASP293 1.5 126.3 1.0 NE2 B:HIS292 1.7 150.1 1.0 NE2 B:HIS256 2.0 122.6 1.0 CG B:ASP402 2.2 126.3 1.0 OD2 B:ASP402 2.6 115.5 1.0 CE1 B:HIS292 2.7 155.3 1.0 CD2 B:HIS292 2.7 161.9 1.0 CG B:ASP293 2.7 136.9 1.0 CE1 B:HIS256 2.8 146.1 1.0 CD2 B:HIS256 3.0 141.4 1.0 CB B:ASP402 3.6 146.8 1.0 OD1 B:ASP293 3.6 113.7 1.0 CB B:ASP293 3.6 131.9 1.0 ND1 B:HIS292 3.7 158.1 1.0 NE2 B:HIS252 3.8 121.4 1.0 CG B:HIS292 3.8 168.0 1.0 CD2 B:HIS252 3.8 124.7 1.0 MG B:MG2002 3.9 59.8 0.0 ND1 B:HIS256 3.9 156.5 1.0 CA B:ASP402 4.0 154.4 1.0 CG B:HIS256 4.1 153.1 1.0 O B:ASP402 4.6 143.8 1.0 C B:ASP402 4.7 158.2 1.0 OG1 B:THR363 4.8 127.2 1.0 CG2 B:VAL260 4.8 156.0 1.0 CA B:ASP293 4.8 131.6 1.0 N B:ASP293 4.9 136.7 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