Zinc in PDB 3jsw: Human PDE9 in Complex with Selective Inhibitor

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

The structure of Human PDE9 in Complex with Selective Inhibitor, PDB code: 3jsw was solved by S.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.278, 103.278, 270.349, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.2

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

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Human PDE9 in Complex with Selective Inhibitor (pdb code 3jsw). 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 Inhibitor, PDB code: 3jsw:
Jump to Zinc binding site number: 1; 2;

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


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 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:68.2 occ:1.00 OD2 A:ASP293 2.2 36.2 1.0 OD1 A:ASP402 2.4 43.2 1.0 O A:HOH512 2.5 33.4 1.0 NE2 A:HIS256 2.6 43.0 1.0 NE2 A:HIS292 2.6 39.5 1.0 CG A:ASP402 3.2 39.7 1.0 CG A:ASP293 3.2 34.3 1.0 CD2 A:HIS292 3.2 36.3 1.0 OD2 A:ASP402 3.3 39.5 1.0 CD2 A:HIS256 3.4 40.3 1.0 CE1 A:HIS256 3.6 40.1 1.0 MG A:MG902 3.6 45.6 1.0 OD1 A:ASP293 3.7 35.9 1.0 CE1 A:HIS292 3.7 39.9 1.0 O A:HOH84 4.0 32.9 1.0 CD2 A:HIS252 4.1 38.0 1.0 O A:HOH533 4.2 42.6 1.0 NE2 A:HIS252 4.2 35.9 1.0 CB A:ASP293 4.3 34.9 1.0 CG A:HIS292 4.4 39.3 1.0 CB A:ASP402 4.5 39.6 1.0 CG A:HIS256 4.6 40.5 1.0 ND1 A:HIS256 4.6 40.2 1.0 ND1 A:HIS292 4.7 41.2 1.0 O A:ASP402 4.8 38.7 1.0 CG2 A:VAL260 4.9 40.9 1.0

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


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 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:74.2 occ:1.00 OD2 B:ASP293 2.3 40.8 1.0 OD1 B:ASP402 2.4 39.8 1.0 NE2 B:HIS292 2.5 41.2 1.0 NE2 B:HIS256 2.5 41.3 1.0 O B:HOH525 2.8 44.8 1.0 CD2 B:HIS292 3.1 40.1 1.0 CG B:ASP402 3.2 38.3 1.0 CG B:ASP293 3.2 38.8 1.0 OD2 B:ASP402 3.3 41.7 1.0 CD2 B:HIS256 3.3 40.4 1.0 CE1 B:HIS256 3.6 40.7 1.0 OD1 B:ASP293 3.7 41.1 1.0 CE1 B:HIS292 3.7 43.1 1.0 MG B:MG902 3.8 40.2 1.0 O B:HOH125 4.0 46.4 1.0 CD2 B:HIS252 4.1 37.8 1.0 NE2 B:HIS252 4.2 37.7 1.0 CB B:ASP293 4.3 36.9 1.0 CG B:HIS292 4.4 41.1 1.0 CG B:HIS256 4.5 41.7 1.0 O B:HOH57 4.6 33.6 1.0 CB B:ASP402 4.6 39.1 1.0 ND1 B:HIS256 4.6 41.7 1.0 ND1 B:HIS292 4.6 42.4 1.0 CG2 B:VAL260 4.7 36.7 1.0 O B:ASP402 4.8 38.7 1.0 CA B:ASP402 5.0 38.8 1.0

P.R.Verhoest, C.Proulx-Lafrance, M.Corman, L.Chenard, C.J.Helal, X.Hou, R.Kleiman, S.Liu, E.Marr, F.S.Menniti, C.J.Schmidt, M.Vanase-Frawley, A.W.Schmidt, R.D.Williams, F.R.Nelson, K.R.Fonseca, S.Liras. Identification of A Brain Penetrant PDE9A Inhibitor Utilizing Prospective Design and Chemical Enablement As A Rapid Lead Optimization Strategy. J.Med.Chem. V. 52 7946 2009.
ISSN: ISSN 0022-2623
PubMed: 19919087
DOI: 10.1021/JM9015334