Zinc in PDB 6znd: [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors

All present enzymatic activity of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors:
3.1.4.17;

The structure of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors, PDB code: 6znd was solved by G.Tresadern, P.M.Leonard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.51 / 2.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	171.060, 69.520, 55.090, 90.00, 91.16, 90.00
R / Rfree (%)	21.5 / 29.1

The structure of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors (pdb code 6znd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors, PDB code: 6znd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:12.4 occ:1.00 O A:HOH1126 1.7 6.4 1.0 OD2 A:ASP697 2.0 7.3 1.0 NE2 A:HIS696 2.0 17.2 1.0 OD1 A:ASP808 2.2 13.1 1.0 NE2 A:HIS660 2.2 14.8 1.0 CD2 A:HIS696 2.8 18.5 1.0 CG A:ASP697 3.0 12.8 1.0 CG A:ASP808 3.1 17.8 1.0 CE1 A:HIS696 3.1 18.0 1.0 CE1 A:HIS660 3.2 16.6 1.0 CD2 A:HIS660 3.2 17.7 1.0 OD2 A:ASP808 3.4 15.1 1.0 OD1 A:ASP697 3.4 9.3 1.0 MG A:MG1002 3.5 2.0 1.0 CG A:HIS696 4.0 15.8 1.0 ND1 A:HIS696 4.1 16.3 1.0 O A:HOH1104 4.2 14.5 1.0 CB A:ASP697 4.2 13.9 1.0 CD2 A:HIS656 4.3 17.0 1.0 ND1 A:HIS660 4.3 13.0 1.0 O A:HOH1173 4.3 11.3 1.0 CG A:HIS660 4.3 16.8 1.0 O A:HOH1114 4.3 3.9 1.0 CB A:ASP808 4.5 19.2 1.0 NE2 A:HIS656 4.6 17.5 1.0 CG2 A:VAL664 4.8 24.2 1.0 CA A:ASP808 4.9 19.9 1.0 O A:HOH1150 4.9 2.5 1.0

Zinc binding site 2 out of 2 in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:9.6 occ:1.00 OD2 B:ASP697 2.0 11.5 1.0 O B:HOH1135 2.0 9.4 1.0 NE2 B:HIS660 2.0 18.7 1.0 NE2 B:HIS696 2.1 14.9 1.0 OD1 B:ASP808 2.2 16.5 1.0 O B:HOH1151 2.3 27.5 1.0 CD2 B:HIS696 2.9 16.4 1.0 CD2 B:HIS660 3.0 18.1 1.0 CE1 B:HIS660 3.1 17.0 1.0 CG B:ASP697 3.1 15.5 1.0 CG B:ASP808 3.1 16.0 1.0 CE1 B:HIS696 3.2 16.0 1.0 OD2 B:ASP808 3.2 14.1 1.0 OD1 B:ASP697 3.6 11.4 1.0 MG B:MG1002 3.8 2.0 1.0 CG B:HIS696 4.1 16.0 1.0 ND1 B:HIS660 4.1 17.5 1.0 O B:HOH1123 4.2 14.7 1.0 CG B:HIS660 4.2 18.6 1.0 CD2 B:HIS656 4.2 24.6 1.0 O B:HOH1133 4.2 13.3 1.0 ND1 B:HIS696 4.2 16.5 1.0 CB B:ASP697 4.3 16.9 1.0 O B:HOH1113 4.4 8.6 1.0 NE2 B:HIS656 4.4 25.3 1.0 CB B:ASP808 4.5 16.2 1.0 CG2 B:VAL664 4.9 18.3 1.0 CA B:ASP808 4.9 16.3 1.0 O B:HOH1112 5.0 9.7 1.0 O B:ASP808 5.0 15.9 1.0

G.Tresadern, I.Velter, A.A.Trabanco, F.Van Den Keybus, G.J.Macdonald, M.V.F.Somers, G.Vanhoof, P.M.Leonard, M.B.A.C.Lamers, Y.E.M.Van Roosbroeck, P.J.J.A.Buijnsters. [1,2,4]Triazolo[1,5- A ]Pyrimidine Phosphodiesterase 2A Inhibitors: Structure and Free-Energy Perturbation-Guided Exploration. J.Med.Chem. V. 63 12887 2020.
ISSN: ISSN 0022-2623
PubMed: 33105987
DOI: 10.1021/ACS.JMEDCHEM.0C01272