Zinc in PDB 3jsi: Human Phosphodiesterase 9 in Complex with Inhibitor

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

The structure of Human Phosphodiesterase 9 in Complex with Inhibitor, PDB code: 3jsi was solved by S.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.65 / 2.72
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.099, 104.099, 271.040, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 21.8

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

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Human Phosphodiesterase 9 in Complex with Inhibitor (pdb code 3jsi). 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 Inhibitor, PDB code: 3jsi:
Jump to Zinc binding site number: 1; 2;

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


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 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:79.2 occ:1.00 OD1 A:ASP402 2.1 53.9 1.0 OD2 A:ASP293 2.1 49.4 1.0 NE2 A:HIS256 2.5 45.0 1.0 NE2 A:HIS292 2.5 39.9 1.0 CD2 A:HIS292 3.1 40.0 1.0 CG A:ASP402 3.1 53.0 1.0 CG A:ASP293 3.2 44.3 1.0 CE1 A:HIS256 3.3 44.9 1.0 OD2 A:ASP402 3.5 59.6 1.0 O A:HOH951 3.5 48.0 1.0 CD2 A:HIS256 3.5 45.3 1.0 OD1 A:ASP293 3.6 45.0 1.0 MG A:MG902 3.7 76.9 1.0 CE1 A:HIS292 3.7 39.5 1.0 CD2 A:HIS252 3.9 41.1 1.0 NE2 A:HIS252 4.0 41.0 1.0 CG A:HIS292 4.4 38.1 1.0 O A:ASP402 4.4 45.4 1.0 CB A:ASP402 4.5 41.6 1.0 CB A:ASP293 4.5 34.9 1.0 ND1 A:HIS256 4.5 45.6 1.0 O A:HOH954 4.6 42.6 1.0 CG A:HIS256 4.6 43.8 1.0 ND1 A:HIS292 4.7 39.9 1.0 CA A:ASP402 4.8 40.0 1.0 O A:HOH952 4.9 41.4 1.0

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


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 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:77.1 occ:1.00 OD1 B:ASP402 2.1 55.4 1.0 OD2 B:ASP293 2.1 52.8 1.0 NE2 B:HIS256 2.5 49.7 1.0 NE2 B:HIS292 2.5 46.3 1.0 CG B:ASP402 3.1 55.0 1.0 CD2 B:HIS292 3.1 46.2 1.0 CG B:ASP293 3.2 45.7 1.0 CE1 B:HIS256 3.3 49.6 1.0 O B:HOH956 3.4 37.4 1.0 OD2 B:ASP402 3.4 62.5 1.0 CD2 B:HIS256 3.5 50.2 1.0 OD1 B:ASP293 3.6 44.9 1.0 O B:HOH955 3.6 53.9 1.0 MG B:MG902 3.7 44.6 1.0 CE1 B:HIS292 3.7 46.2 1.0 CD2 B:HIS252 3.9 43.7 1.0 NE2 B:HIS252 4.0 43.3 1.0 CG B:HIS292 4.4 44.3 1.0 O B:ASP402 4.4 44.8 1.0 CB B:ASP402 4.4 41.7 1.0 CB B:ASP293 4.5 38.8 1.0 O B:HOH959 4.5 29.0 1.0 ND1 B:HIS256 4.5 50.6 1.0 CG B:HIS256 4.6 48.7 1.0 ND1 B:HIS292 4.7 46.6 1.0 CA B:ASP402 4.8 40.1 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