Zinc in PDB 6kdz: Crystal Structure of PDE10A in Complex with A Triazolopyrimidine Inhibitor

All present enzymatic activity of Crystal Structure of PDE10A in Complex with A Triazolopyrimidine Inhibitor:
3.1.4.17; 3.1.4.35;

The structure of Crystal Structure of PDE10A in Complex with A Triazolopyrimidine Inhibitor, PDB code: 6kdz was solved by Y.Amano, K.Honbou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.97 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.218, 81.044, 162.136, 90.00, 90.00, 90.00
R / Rfree (%)	25.3 / 32.5

The structure of Crystal Structure of PDE10A in Complex with A Triazolopyrimidine Inhibitor also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE10A in Complex with A Triazolopyrimidine Inhibitor (pdb code 6kdz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of PDE10A in Complex with A Triazolopyrimidine Inhibitor, PDB code: 6kdz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PDE10A in Complex with A Triazolopyrimidine Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of PDE10A in Complex with A Triazolopyrimidine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:59.2 occ:1.00 OD2 A:ASP564 2.1 60.2 1.0 NE2 A:HIS563 2.2 55.7 1.0 NE2 A:HIS529 2.4 43.2 1.0 OD1 A:ASP674 2.5 64.3 1.0 CD2 A:HIS563 3.0 53.6 1.0 CG A:ASP564 3.0 60.2 1.0 MG A:MG802 3.2 41.3 1.0 CG A:ASP674 3.3 58.3 1.0 OD2 A:ASP674 3.3 59.8 1.0 CD2 A:HIS529 3.3 46.9 1.0 CE1 A:HIS563 3.4 54.9 1.0 CE1 A:HIS529 3.4 47.7 1.0 OD1 A:ASP564 3.4 58.7 1.0 CD2 A:HIS525 4.1 66.5 1.0 CG A:HIS563 4.2 52.1 1.0 CB A:ASP564 4.3 59.5 1.0 ND1 A:HIS563 4.4 53.0 1.0 ND1 A:HIS529 4.5 48.3 1.0 CG A:HIS529 4.6 48.7 1.0 NE2 A:HIS525 4.6 65.5 1.0 CB A:ASP674 4.7 54.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE10A in Complex with A Triazolopyrimidine Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of PDE10A in Complex with A Triazolopyrimidine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:63.5 occ:1.00 NE2 B:HIS529 2.2 39.5 1.0 OD2 B:ASP564 2.2 41.4 1.0 NE2 B:HIS563 2.2 56.1 1.0 OD1 B:ASP674 2.3 41.7 1.0 CD2 B:HIS563 3.1 55.0 1.0 CG B:ASP674 3.1 47.1 1.0 CD2 B:HIS529 3.2 40.6 1.0 CG B:ASP564 3.2 43.5 1.0 CE1 B:HIS529 3.2 41.4 1.0 OD2 B:ASP674 3.2 46.1 1.0 CE1 B:HIS563 3.3 51.7 1.0 MG B:MG802 3.5 34.9 1.0 OD1 B:ASP564 3.6 43.8 1.0 CD2 B:HIS525 4.0 70.7 1.0 CG B:HIS563 4.3 54.0 1.0 ND1 B:HIS529 4.3 37.9 1.0 ND1 B:HIS563 4.3 53.1 1.0 CG B:HIS529 4.4 41.4 1.0 CB B:ASP564 4.4 43.6 1.0 NE2 B:HIS525 4.5 77.6 1.0 CB B:ASP674 4.6 47.6 1.0 O B:ASP674 4.9 52.2 1.0 CA B:ASP674 5.0 49.9 1.0

A.Chino, S.Honda, M.Morita, K.Yonezawa, W.Hamaguchi, Y.Amano, H.Moriguchi, M.Yamazaki, M.Aota, M.Tomishima, N.Masuda. Synthesis, Sar Study, and Biological Evaluation of Novel 2,3-Dihydro-1H-Imidazo[1,2-A]Benzimidazole Derivatives As Phosphodiesterase 10A Inhibitors. Bioorg.Med.Chem. V. 27 3692 2019.
ISSN: ESSN 1464-3391
PubMed: 31301949
DOI: 10.1016/J.BMC.2019.07.010