Zinc in PDB 7f0i: Phosphodiesterase-9A in Complex with Inhibitor 4B

All present enzymatic activity of Phosphodiesterase-9A in Complex with Inhibitor 4B:
3.1.4.35;

The structure of Phosphodiesterase-9A in Complex with Inhibitor 4B, PDB code: 7f0i was solved by Y.Wu, Y.Y.Huang, H.B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.53 / 2.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.467, 103.467, 268.921, 90, 90, 90
R / Rfree (%)	27.1 / 33.4

The structure of Phosphodiesterase-9A in Complex with Inhibitor 4B also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Phosphodiesterase-9A in Complex with Inhibitor 4B (pdb code 7f0i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Phosphodiesterase-9A in Complex with Inhibitor 4B, PDB code: 7f0i:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Phosphodiesterase-9A in Complex with Inhibitor 4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphodiesterase-9A in Complex with Inhibitor 4B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:55.8 occ:1.00 OD1 A:ASP402 2.1 29.7 1.0 OD2 A:ASP293 2.2 28.0 1.0 NE2 A:HIS292 2.4 26.2 1.0 CG A:ASP402 2.8 25.9 1.0 NE2 A:HIS256 2.8 30.5 1.0 OD2 A:ASP402 2.9 24.7 1.0 CD2 A:HIS292 3.0 21.6 1.0 CG A:ASP293 3.3 23.6 1.0 MG A:MG602 3.4 18.0 1.0 CE1 A:HIS292 3.6 21.0 1.0 CE1 A:HIS256 3.7 24.3 1.0 CD2 A:HIS256 3.8 25.3 1.0 OD1 A:ASP293 3.9 21.4 1.0 CB A:ASP402 4.2 27.7 1.0 CD2 A:HIS252 4.2 20.4 1.0 O A:HOH748 4.2 23.2 1.0 O A:HOH718 4.2 26.8 1.0 CG A:HIS292 4.3 17.4 1.0 O A:HOH722 4.3 21.8 1.0 O A:HOH708 4.3 18.0 1.0 CB A:ASP293 4.5 19.6 1.0 ND1 A:HIS292 4.5 20.1 1.0 O A:ASP402 4.7 26.7 1.0 NE2 A:HIS252 4.7 22.1 1.0 ND1 A:HIS256 4.8 20.2 1.0 CA A:ASP402 4.9 22.2 1.0 CG2 A:VAL260 5.0 21.7 1.0 CG A:HIS256 5.0 24.7 1.0

Zinc binding site 2 out of 2 in the Phosphodiesterase-9A in Complex with Inhibitor 4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphodiesterase-9A in Complex with Inhibitor 4B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:38.8 occ:1.00 OD2 B:ASP293 2.2 21.3 1.0 NE2 B:HIS256 2.2 22.0 1.0 OD1 B:ASP402 2.2 19.8 1.0 NE2 B:HIS292 3.0 20.0 1.0 CE1 B:HIS256 3.0 21.9 1.0 CG B:ASP402 3.3 18.2 1.0 CG B:ASP293 3.3 18.6 1.0 CD2 B:HIS256 3.3 21.6 1.0 MG B:MG602 3.3 18.7 1.0 OD2 B:ASP402 3.5 17.3 1.0 CD2 B:HIS292 3.6 17.7 1.0 CE1 B:HIS292 3.7 21.0 1.0 CD2 B:HIS252 3.9 17.4 1.0 O B:HOH738 3.9 13.2 1.0 OD1 B:ASP293 3.9 21.2 1.0 NE2 B:HIS252 4.1 19.0 1.0 O B:HOH741 4.1 20.3 1.0 ND1 B:HIS256 4.2 20.7 1.0 CG B:HIS256 4.4 17.7 1.0 CB B:ASP293 4.4 16.5 1.0 CG B:HIS292 4.5 16.9 1.0 ND1 B:HIS292 4.6 17.9 1.0 O B:ASP402 4.6 21.3 1.0 CB B:ASP402 4.6 21.1 1.0 O B:HOH722 4.7 18.8 1.0 CA B:ASP402 4.9 19.5 1.0 CG2 B:VAL260 5.0 16.9 1.0 O B:HOH724 5.0 23.1 1.0

Y.Wu, Q.Wang, M.Y.Jiang, Y.Y.Huang, Z.Zhu, C.Han, Y.J.Tian, B.Zhang, H.B.Luo. Discovery of Potent Phosphodiesterase-9 Inhibitors For the Treatment of Hepatic Fibrosis J.Med.Chem. V. 64 9537 2021.
ISSN: ISSN 0022-2623
DOI: 10.1021/ACS.JMEDCHEM.1C00862