Zinc in PDB 6cyc: PDE2 in Complex with Compound 5

All present enzymatic activity of PDE2 in Complex with Compound 5:
3.1.4.17;

The structure of PDE2 in Complex with Compound 5, PDB code: 6cyc was solved by J.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.17 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.250, 96.410, 101.650, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 20.5

The structure of PDE2 in Complex with Compound 5 also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Zinc atom in the PDE2 in Complex with Compound 5 (pdb code 6cyc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the PDE2 in Complex with Compound 5, PDB code: 6cyc:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the PDE2 in Complex with Compound 5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PDE2 in Complex with Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:17.6 occ:1.00 NE2 A:HIS660 2.1 12.8 1.0 OD1 A:ASP808 2.1 11.2 1.0 OD2 A:ASP697 2.1 12.9 1.0 NE2 A:HIS696 2.1 12.6 1.0 O A:HOH1192 2.2 13.6 1.0 O A:HOH1101 2.5 13.2 1.0 CE1 A:HIS660 3.0 12.5 1.0 CG A:ASP808 3.0 14.8 1.0 CD2 A:HIS696 3.0 13.3 1.0 CE1 A:HIS696 3.1 13.2 1.0 CD2 A:HIS660 3.1 13.2 1.0 CG A:ASP697 3.1 13.2 1.0 OD2 A:ASP808 3.3 15.5 1.0 OD1 A:ASP697 3.7 12.3 1.0 O A:HOH1181 4.1 13.1 1.0 MG A:MG1002 4.1 13.8 1.0 ND1 A:HIS660 4.2 13.6 1.0 CG A:HIS696 4.2 14.1 1.0 CD2 A:HIS656 4.2 14.4 1.0 CG A:HIS660 4.2 12.2 1.0 NE2 A:HIS656 4.2 14.1 1.0 ND1 A:HIS696 4.2 14.3 1.0 O A:HOH1218 4.3 13.1 1.0 CB A:ASP697 4.3 12.5 1.0 CB A:ASP808 4.4 13.1 1.0 CG2 A:VAL664 4.8 15.7 1.0 CA A:ASP808 4.8 13.5 1.0 O A:HOH1104 4.8 13.9 1.0 O A:ASP808 4.9 15.4 1.0

Zinc binding site 2 out of 2 in the PDE2 in Complex with Compound 5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of PDE2 in Complex with Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:17.7 occ:1.00 NE2 B:HIS660 2.0 14.0 1.0 OD2 B:ASP697 2.0 13.3 1.0 NE2 B:HIS696 2.1 13.5 1.0 OD1 B:ASP808 2.1 13.0 1.0 O B:HOH1206 2.2 13.3 1.0 O B:HOH1110 2.6 13.1 1.0 CE1 B:HIS660 3.0 13.6 1.0 CD2 B:HIS696 3.1 14.1 1.0 CE1 B:HIS696 3.1 13.8 1.0 CG B:ASP808 3.1 16.9 1.0 CD2 B:HIS660 3.1 14.1 1.0 CG B:ASP697 3.1 14.3 1.0 OD2 B:ASP808 3.4 16.2 1.0 OD1 B:ASP697 3.7 13.6 1.0 O B:HOH1184 4.0 13.2 1.0 MG B:MG1002 4.1 14.6 1.0 ND1 B:HIS660 4.2 15.1 1.0 CG B:HIS696 4.2 14.3 1.0 CG B:HIS660 4.2 13.2 1.0 CD2 B:HIS656 4.2 15.3 1.0 ND1 B:HIS696 4.2 15.1 1.0 CB B:ASP697 4.3 13.5 1.0 O B:HOH1269 4.3 13.6 1.0 NE2 B:HIS656 4.3 14.5 1.0 CB B:ASP808 4.4 12.5 1.0 CG2 B:VAL664 4.7 13.0 1.0 CA B:ASP808 4.8 10.9 1.0 O B:HOH1104 4.9 12.8 1.0 O B:ASP808 4.9 13.9 1.0

S.J.Stachel, R.Berger, A.B.Nomland, A.T.Ginnetti, D.V.Paone, D.Wang, V.Puri, H.Lange, J.Drott, J.Lu, J.Marcus, M.P.Dwyer, S.Suon, J.M.Uslaner, S.M.Smith. Structure-Guided Design and Procognitive Assessment of A Potent and Selective Phosphodiesterase 2A Inhibitor. Acs Med Chem Lett V. 9 815 2018.
ISSN: ISSN 1948-5875
PubMed: 30128073
DOI: 10.1021/ACSMEDCHEMLETT.8B00214