Zinc in PDB 6kdx: 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: 6kdx 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)	26.66 / 2.44
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.417, 81.440, 159.976, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 30.1

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 6kdx). 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: 6kdx:
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:51.4 occ:1.00 OD1 A:ASP674 2.1 37.9 1.0 NE2 A:HIS529 2.1 32.3 1.0 NE2 A:HIS563 2.2 49.3 1.0 OD2 A:ASP564 2.2 39.0 1.0 O A:HOH903 2.6 36.6 1.0 CG A:ASP674 3.0 39.2 1.0 O A:HOH907 3.0 46.1 1.0 CD2 A:HIS563 3.0 44.3 1.0 CD2 A:HIS529 3.1 34.3 1.0 CE1 A:HIS529 3.1 35.9 1.0 OD2 A:ASP674 3.2 45.8 1.0 CG A:ASP564 3.2 46.6 1.0 CE1 A:HIS563 3.2 44.2 1.0 OD1 A:ASP564 3.6 45.4 1.0 O A:HOH910 3.6 36.3 1.0 O A:HOH904 3.8 33.8 1.0 MG A:MG802 4.0 43.8 1.0 CD2 A:HIS525 4.2 45.9 1.0 CG A:HIS563 4.3 52.0 1.0 ND1 A:HIS529 4.3 32.8 1.0 CG A:HIS529 4.3 32.5 1.0 ND1 A:HIS563 4.3 50.5 1.0 CB A:ASP674 4.4 37.3 1.0 CB A:ASP564 4.4 45.5 1.0 NE2 A:HIS525 4.7 45.5 1.0 O A:ASP674 4.7 37.8 1.0 CG2 A:VAL533 4.8 32.7 1.0 CA A:ASP674 4.8 40.7 1.0 O A:HOH906 4.8 40.0 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:39.2 occ:1.00 O B:HOH907 1.9 34.7 1.0 NE2 B:HIS529 2.0 37.2 1.0 NE2 B:HIS563 2.1 39.8 1.0 O B:HOH909 2.1 27.1 1.0 OD1 B:ASP674 2.2 32.9 1.0 OD2 B:ASP564 2.2 28.7 1.0 CD2 B:HIS529 2.9 32.4 1.0 CE1 B:HIS563 3.0 43.7 1.0 CD2 B:HIS563 3.1 42.2 1.0 CG B:ASP674 3.1 36.1 1.0 CE1 B:HIS529 3.1 33.0 1.0 CG B:ASP564 3.1 31.0 1.0 OD2 B:ASP674 3.3 40.3 1.0 OD1 B:ASP564 3.4 30.4 1.0 O B:HOH906 3.7 32.8 1.0 MG B:MG802 3.7 34.8 1.0 O B:HOH908 4.0 36.8 1.0 O B:HOH905 4.1 30.9 1.0 CG B:HIS529 4.1 32.5 1.0 CD2 B:HIS525 4.1 45.2 1.0 ND1 B:HIS529 4.2 32.7 1.0 ND1 B:HIS563 4.2 39.6 1.0 CG B:HIS563 4.2 38.9 1.0 CB B:ASP564 4.4 29.0 1.0 CB B:ASP674 4.5 40.0 1.0 NE2 B:HIS525 4.7 44.8 1.0 O B:HOH903 4.8 28.8 1.0 CG2 B:VAL533 4.8 29.5 1.0 CA B:ASP674 4.8 34.4 1.0 O B:ASP674 4.9 32.9 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