Zinc in PDB 6cyd: PDE2 in Complex with Compound 7

All present enzymatic activity of PDE2 in Complex with Compound 7:
3.1.4.17;

The structure of PDE2 in Complex with Compound 7, PDB code: 6cyd was solved by J.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.91 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.940, 91.820, 102.830, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21

The structure of PDE2 in Complex with Compound 7 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 7 (pdb code 6cyd). 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 7, PDB code: 6cyd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the PDE2 in Complex with Compound 7


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 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:19.7 occ:1.00 OD2 A:ASP697 2.0 12.8 1.0 NE2 A:HIS660 2.1 15.5 1.0 NE2 A:HIS696 2.1 14.8 1.0 OD1 A:ASP808 2.1 11.4 1.0 O A:HOH1218 2.3 16.5 1.0 O A:HOH1101 2.6 14.6 1.0 CD2 A:HIS696 3.0 15.2 1.0 CE1 A:HIS660 3.0 16.0 1.0 CG A:ASP808 3.1 16.3 1.0 CG A:ASP697 3.1 14.2 1.0 CD2 A:HIS660 3.1 16.5 1.0 CE1 A:HIS696 3.2 14.8 1.0 OD2 A:ASP808 3.4 16.7 1.0 OD1 A:ASP697 3.6 15.2 1.0 MG A:MG1002 4.0 16.2 1.0 O A:HOH1210 4.0 14.2 1.0 CD2 A:HIS656 4.2 16.9 1.0 CG A:HIS696 4.2 15.5 1.0 ND1 A:HIS660 4.2 16.1 1.0 CG A:HIS660 4.2 15.4 1.0 ND1 A:HIS696 4.3 15.1 1.0 CB A:ASP697 4.3 12.3 1.0 O A:HOH1223 4.3 18.1 1.0 NE2 A:HIS656 4.3 16.4 1.0 CB A:ASP808 4.5 15.0 1.0 CG2 A:VAL664 4.7 16.5 1.0 O A:HOH1106 4.7 14.1 1.0 CA A:ASP808 4.8 14.0 1.0 O A:ASP808 4.9 15.3 1.0

Zinc binding site 2 out of 2 in the PDE2 in Complex with Compound 7


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 7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:20.8 occ:1.00 NE2 B:HIS660 2.0 16.0 1.0 OD2 B:ASP697 2.1 15.6 1.0 NE2 B:HIS696 2.1 15.7 1.0 OD1 B:ASP808 2.2 14.6 1.0 O B:HOH1186 2.3 16.6 1.0 O B:HOH1102 2.4 16.3 1.0 CE1 B:HIS660 3.0 16.2 1.0 CD2 B:HIS696 3.0 15.6 1.0 CG B:ASP808 3.1 18.9 1.0 CD2 B:HIS660 3.1 16.5 1.0 CG B:ASP697 3.1 15.0 1.0 CE1 B:HIS696 3.2 16.1 1.0 OD2 B:ASP808 3.4 18.5 1.0 OD1 B:ASP697 3.7 15.7 1.0 MG B:MG1002 4.0 18.3 1.0 O B:HOH1202 4.1 17.7 1.0 ND1 B:HIS660 4.2 16.4 1.0 CD2 B:HIS656 4.2 18.1 1.0 CG B:HIS696 4.2 14.5 1.0 CG B:HIS660 4.2 15.5 1.0 O B:HOH1239 4.3 15.1 1.0 NE2 B:HIS656 4.3 18.3 1.0 CB B:ASP697 4.3 13.2 1.0 ND1 B:HIS696 4.3 15.6 1.0 CB B:ASP808 4.5 13.1 1.0 CG2 B:VAL664 4.7 15.7 1.0 O B:HOH1103 4.8 16.7 1.0 CA B:ASP808 4.8 12.9 1.0 O B:ASP808 4.9 15.1 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