Zinc in PDB 6a3n: Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2

All present enzymatic activity of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2:
3.1.4.35;

The structure of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2, PDB code: 6a3n was solved by Y.N.Wu, Q.Zhou, Y.P.Chen, H.B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.46 / 2.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.110, 104.110, 269.079, 90.00, 90.00, 90.00
R / Rfree (%)	24.8 / 28

The structure of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2 also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2 (pdb code 6a3n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2, PDB code: 6a3n:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:51.9 occ:1.00 O A:HOH703 2.0 51.5 1.0 O A:HOH701 2.0 38.3 1.0 OD2 A:ASP293 2.0 31.9 1.0 OD1 A:ASP402 2.0 33.3 1.0 NE2 A:HIS292 2.1 35.4 1.0 NE2 A:HIS256 2.2 39.7 1.0 CE1 A:HIS292 3.1 32.7 1.0 CD2 A:HIS292 3.1 31.9 1.0 CG A:ASP402 3.1 27.8 1.0 CE1 A:HIS256 3.1 34.9 1.0 CD2 A:HIS256 3.2 35.5 1.0 CG A:ASP293 3.2 26.0 1.0 OD2 A:ASP402 3.6 28.3 1.0 OD1 A:ASP293 3.8 26.9 1.0 MG A:MG602 3.9 28.3 1.0 CD2 A:HIS252 4.0 24.2 1.0 ND1 A:HIS292 4.2 31.7 1.0 NE2 A:HIS252 4.2 24.5 1.0 CG A:HIS292 4.2 29.6 1.0 ND1 A:HIS256 4.2 32.9 1.0 CG A:HIS256 4.3 32.3 1.0 O A:HOH705 4.3 22.7 1.0 CB A:ASP293 4.4 24.1 1.0 O A:ASP402 4.4 27.7 1.0 CB A:ASP402 4.4 26.7 1.0 O A:HOH702 4.5 26.8 1.0 O A:HOH737 4.5 27.4 1.0 CA A:ASP402 4.7 25.8 1.0 CG2 A:VAL260 4.7 21.6 1.0 C A:ASP402 5.0 26.8 1.0 O A:HOH772 5.0 26.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:44.1 occ:1.00 O B:HOH707 2.0 47.1 1.0 O B:HOH702 2.0 31.1 1.0 OD2 B:ASP293 2.0 28.6 1.0 OD1 B:ASP402 2.0 32.1 1.0 NE2 B:HIS292 2.1 30.1 1.0 NE2 B:HIS256 2.1 36.0 1.0 CD2 B:HIS292 3.1 27.2 1.0 CE1 B:HIS256 3.1 33.6 1.0 CG B:ASP402 3.1 26.7 1.0 CE1 B:HIS292 3.1 27.4 1.0 CG B:ASP293 3.1 24.3 1.0 CD2 B:HIS256 3.1 32.8 1.0 OD2 B:ASP402 3.6 26.7 1.0 OD1 B:ASP293 3.8 24.1 1.0 MG B:MG602 3.9 22.3 1.0 O B:HOH723 4.0 23.0 1.0 ND1 B:HIS292 4.2 26.3 1.0 ND1 B:HIS256 4.2 32.2 1.0 CG B:HIS292 4.2 25.3 1.0 CB B:ASP293 4.3 23.2 1.0 CD2 B:HIS252 4.3 22.4 1.0 CG B:HIS256 4.3 30.5 1.0 CB B:ASP402 4.4 25.7 1.0 O B:HOH701 4.5 20.8 1.0 NE2 B:HIS252 4.5 22.3 1.0 O B:ASP402 4.7 23.3 1.0 CA B:ASP402 4.7 23.9 1.0 CG2 B:VAL260 4.8 21.3 1.0 O B:HOH738 4.9 20.1 1.0 O B:HOH733 4.9 18.5 1.0

Y.Wu, Q.Zhou, T.Zhang, Z.Li, Y.P.Chen, P.Zhang, Y.F.Yu, H.Geng, Y.J.Tian, C.Zhang, Y.Wang, J.W.Chen, Y.Chen, H.B.Luo. Discovery of Potent, Selective, and Orally Bioavailable Inhibitors Against Phosphodiesterase-9, A Novel Target For the Treatment of Vascular Dementia. J. Med. Chem. V. 62 4218 2019.
ISSN: ISSN 1520-4804
PubMed: 30916555
DOI: 10.1021/ACS.JMEDCHEM.8B01041