Zinc in PDB 3ws9: Crystal Structure of PDE10A in Complex with A Benzimdazole Inhibitor

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

The structure of Crystal Structure of PDE10A in Complex with A Benzimdazole Inhibitor, PDB code: 3ws9 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)	29.50 / 2.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.421, 81.542, 161.255, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 34.6

The structure of Crystal Structure of PDE10A in Complex with A Benzimdazole 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 Benzimdazole Inhibitor (pdb code 3ws9). 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 Benzimdazole Inhibitor, PDB code: 3ws9:
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 Benzimdazole 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 Benzimdazole Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:37.0 occ:1.00 OD2 A:ASP564 1.9 39.0 1.0 NE2 A:HIS529 2.2 31.9 1.0 NE2 A:HIS563 2.3 41.0 1.0 OD1 A:ASP674 2.4 31.6 1.0 OD2 A:ASP674 2.9 37.2 1.0 CG A:ASP564 2.9 35.5 1.0 CD2 A:HIS563 3.0 40.2 1.0 CG A:ASP674 3.0 32.3 1.0 O A:HOH902 3.1 7.7 1.0 CE1 A:HIS529 3.1 33.5 1.0 CD2 A:HIS529 3.2 33.3 1.0 OD1 A:ASP564 3.3 36.6 1.0 CE1 A:HIS563 3.5 39.5 1.0 MG A:MG802 3.5 19.7 1.0 CD2 A:HIS525 3.7 41.1 1.0 NE2 A:HIS525 3.9 42.1 1.0 CB A:ASP564 4.1 33.2 1.0 CG A:HIS563 4.2 36.1 1.0 ND1 A:HIS529 4.2 33.1 1.0 O A:HOH901 4.3 44.5 1.0 CG A:HIS529 4.3 32.0 1.0 ND1 A:HIS563 4.4 37.3 1.0 CB A:ASP674 4.4 30.1 1.0 O A:ASP674 4.8 32.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE10A in Complex with A Benzimdazole 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 Benzimdazole Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:34.6 occ:1.00 OD2 B:ASP564 1.8 34.0 1.0 NE2 B:HIS563 2.0 32.9 1.0 NE2 B:HIS529 2.1 30.6 1.0 OD1 B:ASP674 2.3 24.0 1.0 OD2 B:ASP674 2.7 22.7 1.0 CG B:ASP674 2.9 23.2 1.0 CD2 B:HIS563 2.9 32.2 1.0 O B:HOH903 3.0 22.9 1.0 CG B:ASP564 3.0 33.2 1.0 CD2 B:HIS529 3.0 31.9 1.0 CE1 B:HIS563 3.0 32.3 1.0 MG B:MG802 3.1 14.2 1.0 CE1 B:HIS529 3.2 31.9 1.0 OD1 B:ASP564 3.7 35.5 1.0 CD2 B:HIS525 3.8 42.0 1.0 CB B:ASP564 3.9 31.8 1.0 CG B:HIS563 4.1 31.3 1.0 ND1 B:HIS563 4.1 30.3 1.0 CG B:HIS529 4.2 32.7 1.0 NE2 B:HIS525 4.2 41.8 1.0 ND1 B:HIS529 4.3 32.5 1.0 CB B:ASP674 4.3 23.4 1.0 O B:HOH901 4.7 19.4 1.0 O B:HOH902 4.8 17.6 1.0 CA B:ASP674 4.9 24.2 1.0 O B:ASP674 5.0 23.4 1.0 CG B:HIS525 5.0 39.0 1.0

A.Chino, N.Masuda, Y.Amano, K.Honbou, T.Mihara, M.Yamazaki, M.Tomishima. Novel Benzimidazole Derivatives As Phosphodiesterase 10A (PDE10A) Inhibitors with Improved Metabolic Stability. Bioorg.Med.Chem. 2014.
ISSN: ESSN 1464-3391
PubMed: 24837154
DOI: 10.1016/J.BMC.2014.04.023