Zinc in PDB 4e90: Human Phosphodiesterase 9 in Complex with Inhibitors

All present enzymatic activity of Human Phosphodiesterase 9 in Complex with Inhibitors:
3.1.4.35;

The structure of Human Phosphodiesterase 9 in Complex with Inhibitors, PDB code: 4e90 was solved by S.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.00 / 2.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.579, 103.579, 270.214, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 21.6

The structure of Human Phosphodiesterase 9 in Complex with Inhibitors also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Human Phosphodiesterase 9 in Complex with Inhibitors (pdb code 4e90). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Phosphodiesterase 9 in Complex with Inhibitors, PDB code: 4e90:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Phosphodiesterase 9 in Complex with Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Phosphodiesterase 9 in Complex with Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:44.9 occ:1.00 OD2 A:ASP293 2.2 32.1 1.0 OD1 A:ASP402 2.2 33.8 1.0 NE2 A:HIS292 2.3 28.6 1.0 NE2 A:HIS256 2.4 30.0 1.0 O A:HOH1137 2.4 28.1 1.0 CD2 A:HIS292 3.0 28.5 1.0 CG A:ASP402 3.1 29.7 1.0 CG A:ASP293 3.1 25.8 1.0 CD2 A:HIS256 3.3 29.8 1.0 OD2 A:ASP402 3.4 29.3 1.0 CE1 A:HIS256 3.4 29.7 1.0 CE1 A:HIS292 3.5 28.5 1.0 MG A:MG902 3.6 32.7 1.0 OD1 A:ASP293 3.6 26.2 1.0 O A:HOH1016 4.1 29.1 1.0 CD2 A:HIS252 4.2 27.0 1.0 CG A:HIS292 4.2 26.6 1.0 O A:HOH1041 4.3 24.7 1.0 CB A:ASP293 4.3 23.2 1.0 NE2 A:HIS252 4.4 26.8 1.0 CG A:HIS256 4.5 28.3 1.0 CB A:ASP402 4.5 24.4 1.0 ND1 A:HIS292 4.5 28.7 1.0 ND1 A:HIS256 4.5 30.3 1.0 O A:HOH1168 4.7 30.2 1.0 O A:ASP402 4.7 29.1 1.0 CG2 A:VAL260 4.8 25.4 1.0 CA A:ASP402 4.9 23.4 1.0

Zinc binding site 2 out of 2 in the Human Phosphodiesterase 9 in Complex with Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Phosphodiesterase 9 in Complex with Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:47.4 occ:1.00 OD2 B:ASP293 2.2 32.1 1.0 OD1 B:ASP402 2.2 27.5 1.0 NE2 B:HIS292 2.3 29.2 1.0 NE2 B:HIS256 2.4 31.0 1.0 O B:HOH1065 2.6 32.8 1.0 CD2 B:HIS292 3.0 28.9 1.0 CG B:ASP402 3.1 28.4 1.0 CG B:ASP293 3.1 27.6 1.0 CD2 B:HIS256 3.3 31.2 1.0 OD2 B:ASP402 3.4 34.8 1.0 CE1 B:HIS256 3.4 30.8 1.0 CE1 B:HIS292 3.5 29.0 1.0 OD1 B:ASP293 3.6 27.8 1.0 MG B:MG902 3.8 38.7 1.0 O B:HOH1082 4.1 33.6 1.0 O B:HOH1028 4.1 25.7 1.0 CD2 B:HIS252 4.2 30.5 1.0 CG B:HIS292 4.3 27.9 1.0 CB B:ASP293 4.3 25.1 1.0 NE2 B:HIS252 4.4 30.4 1.0 CG B:HIS256 4.4 30.2 1.0 CB B:ASP402 4.5 26.5 1.0 ND1 B:HIS292 4.5 29.4 1.0 ND1 B:HIS256 4.5 31.9 1.0 O B:ASP402 4.7 33.1 1.0 CG2 B:VAL260 4.8 25.5 1.0 CA B:ASP402 5.0 25.9 1.0

M.M.Claffey, C.J.Helal, P.R.Verhoest, Z.Kang, K.S.Fors, S.Jung, J.Zhong, M.W.Bundesmann, X.Hou, S.Lui, R.J.Kleiman, M.Vanase-Frawley, A.W.Schmidt, F.Menniti, C.J.Schmidt, W.E.Hoffman, M.Hajos, L.Mcdowell, R.E.O'connor, M.Macdougall-Murphy, K.R.Fonseca, S.L.Becker, F.R.Nelson, S.Liras. Application of Structure-Based Drug Design and Parallel Chemistry to Identify Selective, Brain Penetrant, in Vivo Active Phosphodiesterase 9A Inhibitors. J.Med.Chem. V. 55 9055 2012.
ISSN: ISSN 0022-2623
PubMed: 23025719
DOI: 10.1021/JM3009635