Zinc in PDB 6zqz: [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: 6zqz 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)	87.07 / 1.88
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	55.960, 73.460, 92.230, 109.16, 91.37, 91.26
R / Rfree (%)	19.6 / 24.4

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

Fluorine	(F)	8 atoms
Magnesium	(Mg)	5 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors (pdb code 6zqz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors, PDB code: 6zqz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 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:13.7 occ:1.00 O A:HOH1200 2.0 9.7 1.0 OD2 A:ASP697 2.1 8.9 1.0 NE2 A:HIS696 2.1 8.9 1.0 NE2 A:HIS660 2.1 8.7 1.0 OD1 A:ASP808 2.2 11.2 1.0 O A:HOH1201 2.6 18.3 1.0 CD2 A:HIS696 3.0 8.7 1.0 CD2 A:HIS660 3.1 9.0 1.0 CG A:ASP808 3.1 11.8 1.0 CG A:ASP697 3.2 8.9 1.0 CE1 A:HIS696 3.2 8.9 1.0 CE1 A:HIS660 3.2 9.1 1.0 OD2 A:ASP808 3.3 12.5 1.0 OD1 A:ASP697 3.7 8.7 1.0 MG A:MG1002 3.7 11.2 1.0 O A:HOH1183 4.1 9.2 1.0 CD2 A:HIS656 4.2 10.8 1.0 O A:HOH1194 4.2 15.4 1.0 CG A:HIS696 4.2 8.9 1.0 ND1 A:HIS696 4.3 8.9 1.0 CG A:HIS660 4.3 9.3 1.0 ND1 A:HIS660 4.3 8.9 1.0 CB A:ASP697 4.4 9.0 1.0 NE2 A:HIS656 4.4 11.2 1.0 CB A:ASP808 4.5 11.4 1.0 O A:HOH1141 4.6 8.4 1.0 O A:ASP808 4.9 10.4 1.0 CA A:ASP808 4.9 11.3 1.0 CG2 A:VAL664 5.0 8.8 1.0

Zinc binding site 2 out of 4 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:15.0 occ:1.00 OD2 B:ASP697 2.1 9.9 1.0 O B:HOH1124 2.1 10.4 1.0 NE2 B:HIS660 2.1 11.0 1.0 OD1 B:ASP808 2.2 13.4 1.0 NE2 B:HIS696 2.2 10.6 1.0 O B:HOH1215 2.8 21.9 1.0 CD2 B:HIS696 3.0 10.2 1.0 CD2 B:HIS660 3.0 11.2 1.0 CG B:ASP808 3.1 14.4 1.0 CG B:ASP697 3.1 10.3 1.0 CE1 B:HIS660 3.1 11.0 1.0 OD2 B:ASP808 3.3 14.4 1.0 CE1 B:HIS696 3.3 10.4 1.0 OD1 B:ASP697 3.6 9.6 1.0 MG B:MG1002 3.7 12.3 1.0 O B:HOH1160 3.9 9.5 1.0 O B:HOH1217 4.2 19.9 1.0 CD2 B:HIS656 4.2 12.9 1.0 CG B:HIS696 4.3 10.2 1.0 CG B:HIS660 4.3 11.3 1.0 ND1 B:HIS660 4.3 11.0 1.0 CB B:ASP697 4.3 10.5 1.0 ND1 B:HIS696 4.4 10.0 1.0 CB B:ASP808 4.5 13.9 1.0 NE2 B:HIS656 4.5 13.2 1.0 O B:HOH1119 4.5 10.8 1.0 CG2 B:VAL664 4.9 12.9 1.0 CA B:ASP808 4.9 13.8 1.0 O B:ASP808 4.9 13.8 1.0

Zinc binding site 3 out of 4 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 3 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:15.4 occ:1.00 O C:HOH1105 2.0 12.2 1.0 OD2 C:ASP697 2.0 11.0 1.0 OD1 C:ASP808 2.1 13.6 1.0 NE2 C:HIS696 2.2 11.7 1.0 NE2 C:HIS660 2.2 12.3 1.0 O C:HOH1127 2.3 15.9 1.0 CD2 C:HIS696 2.9 11.1 1.0 CG C:ASP808 3.0 15.0 1.0 CG C:ASP697 3.1 11.1 1.0 CE1 C:HIS660 3.1 12.3 1.0 OD2 C:ASP808 3.2 14.2 1.0 CD2 C:HIS660 3.2 12.3 1.0 CE1 C:HIS696 3.3 10.9 1.0 OD1 C:ASP697 3.5 10.1 1.0 MG C:MG1002 3.7 10.2 1.0 O C:HOH1192 4.0 16.9 1.0 O C:HOH1171 4.0 10.9 1.0 CD2 C:HIS656 4.1 12.7 1.0 CG C:HIS696 4.2 11.3 1.0 ND1 C:HIS660 4.3 12.5 1.0 CB C:ASP697 4.3 11.3 1.0 ND1 C:HIS696 4.3 11.0 1.0 NE2 C:HIS656 4.3 13.2 1.0 CG C:HIS660 4.4 12.6 1.0 CB C:ASP808 4.4 15.8 1.0 O C:HOH1135 4.6 9.4 1.0 CA C:ASP808 4.9 15.9 1.0 CG2 C:VAL664 4.9 13.4 1.0

Zinc binding site 4 out of 4 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 4 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:14.5 occ:1.00 O D:HOH1119 2.0 9.3 1.0 OD2 D:ASP697 2.1 9.5 1.0 NE2 D:HIS660 2.1 11.4 1.0 NE2 D:HIS696 2.1 11.2 1.0 OD1 D:ASP808 2.1 11.9 1.0 O D:HOH1238 2.3 18.6 1.0 CD2 D:HIS696 3.0 10.7 1.0 CD2 D:HIS660 3.0 12.0 1.0 CG D:ASP808 3.0 12.6 1.0 CG D:ASP697 3.1 10.3 1.0 CE1 D:HIS660 3.2 11.5 1.0 CE1 D:HIS696 3.2 10.9 1.0 OD2 D:ASP808 3.2 13.5 1.0 OD1 D:ASP697 3.7 9.7 1.0 MG D:MG1002 3.7 11.8 1.0 O D:HOH1278 4.1 16.9 1.0 CD2 D:HIS656 4.1 14.9 1.0 O D:HOH1226 4.2 9.9 1.0 CG D:HIS696 4.2 10.9 1.0 CG D:HIS660 4.2 11.7 1.0 ND1 D:HIS696 4.3 11.1 1.0 ND1 D:HIS660 4.3 11.7 1.0 CB D:ASP697 4.3 10.7 1.0 NE2 D:HIS656 4.3 14.8 1.0 CB D:ASP808 4.5 12.4 1.0 O D:HOH1127 4.6 12.0 1.0 CA D:ASP808 4.9 12.8 1.0 CG2 D:VAL664 4.9 11.4 1.0 O D:ASP808 5.0 12.1 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