Zinc in PDB 4g2j: Human PDE9 in Complex with Selective Compound

All present enzymatic activity of Human PDE9 in Complex with Selective Compound:
3.1.4.35;

The structure of Human PDE9 in Complex with Selective Compound, PDB code: 4g2j was solved by S.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.36 / 2.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.688, 103.688, 270.075, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 21.3

The structure of Human PDE9 in Complex with Selective Compound also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Human PDE9 in Complex with Selective Compound (pdb code 4g2j). 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 PDE9 in Complex with Selective Compound, PDB code: 4g2j:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human PDE9 in Complex with Selective Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human PDE9 in Complex with Selective Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:52.9 occ:1.00 OD2 A:ASP293 2.1 35.7 1.0 OD1 A:ASP402 2.1 33.4 1.0 NE2 A:HIS292 2.3 33.8 1.0 NE2 A:HIS256 2.3 35.3 1.0 O A:HOH1029 2.4 36.0 1.0 CD2 A:HIS292 3.0 33.6 1.0 CG A:ASP402 3.1 32.5 1.0 CG A:ASP293 3.1 31.2 1.0 CD2 A:HIS256 3.2 35.5 1.0 CE1 A:HIS256 3.3 34.9 1.0 OD2 A:ASP402 3.4 38.4 1.0 CE1 A:HIS292 3.5 33.4 1.0 OD1 A:ASP293 3.7 29.6 1.0 MG A:MG902 3.8 37.0 1.0 O A:HOH1028 4.0 39.1 1.0 CD2 A:HIS252 4.1 34.1 1.0 CG A:HIS292 4.2 31.9 1.0 O A:HOH1100 4.2 37.8 1.0 CB A:ASP293 4.3 28.3 1.0 NE2 A:HIS252 4.3 33.9 1.0 CG A:HIS256 4.4 34.5 1.0 CB A:ASP402 4.4 29.4 1.0 ND1 A:HIS256 4.4 35.9 1.0 ND1 A:HIS292 4.4 33.7 1.0 O A:ASP402 4.7 33.2 1.0 CG2 A:VAL260 4.7 31.6 1.0 O A:HOH1035 4.8 32.5 1.0 CA A:ASP402 4.9 28.4 1.0

Zinc binding site 2 out of 2 in the Human PDE9 in Complex with Selective Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human PDE9 in Complex with Selective Compound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:57.5 occ:1.00 OD2 B:ASP293 2.1 46.7 1.0 OD1 B:ASP402 2.1 35.5 1.0 NE2 B:HIS292 2.3 36.9 1.0 NE2 B:HIS256 2.3 34.8 1.0 O B:HOH1164 2.6 42.2 1.0 CD2 B:HIS292 3.0 36.7 1.0 CG B:ASP402 3.1 37.0 1.0 CG B:ASP293 3.1 36.9 1.0 CD2 B:HIS256 3.3 35.2 1.0 CE1 B:HIS256 3.3 34.7 1.0 OD2 B:ASP402 3.4 43.6 1.0 CE1 B:HIS292 3.5 36.5 1.0 OD1 B:ASP293 3.7 34.1 1.0 MG B:MG902 3.8 39.2 1.0 O B:HOH1050 3.8 43.2 1.0 CD2 B:HIS252 4.1 36.2 1.0 O B:HOH1121 4.1 37.8 1.0 CG B:HIS292 4.2 34.8 1.0 CB B:ASP293 4.3 32.8 1.0 NE2 B:HIS252 4.3 36.0 1.0 CG B:HIS256 4.4 34.0 1.0 CB B:ASP402 4.4 32.7 1.0 ND1 B:HIS256 4.5 35.7 1.0 ND1 B:HIS292 4.5 36.8 1.0 O B:ASP402 4.7 36.9 1.0 CG2 B:VAL260 4.8 32.7 1.0 CA B:ASP402 4.9 31.5 1.0 O B:HOH1064 5.0 37.4 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