Zinc in PDB 6iji: Crystal Structure of PDE10 in Complex with Inhibitor 2B

All present enzymatic activity of Crystal Structure of PDE10 in Complex with Inhibitor 2B:
3.1.4.17; 3.1.4.35;

The structure of Crystal Structure of PDE10 in Complex with Inhibitor 2B, PDB code: 6iji was solved by Y.Y.Huang, Y.F.Yu, C.Zhang, D.Wu, Y.Wu, H.B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.53 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.941, 159.455, 81.650, 90.00, 90.00, 90.00
R / Rfree (%)	25.8 / 34.1

The structure of Crystal Structure of PDE10 in Complex with Inhibitor 2B also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE10 in Complex with Inhibitor 2B (pdb code 6iji). 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 PDE10 in Complex with Inhibitor 2B, PDB code: 6iji:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PDE10 in Complex with Inhibitor 2B


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 PDE10 in Complex with Inhibitor 2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:48.1 occ:1.00 OD1 A:ASP674 2.0 25.7 1.0 OD2 A:ASP564 2.0 36.3 1.0 NE2 A:HIS563 2.1 38.6 1.0 O A:HOH912 2.3 15.8 1.0 NE2 A:HIS529 2.4 26.2 1.0 CD2 A:HIS563 3.0 38.3 1.0 CG A:ASP674 3.0 26.8 1.0 CE1 A:HIS563 3.1 38.4 1.0 CG A:ASP564 3.1 36.4 1.0 CD2 A:HIS529 3.1 26.3 1.0 OD2 A:ASP674 3.3 26.8 1.0 CE1 A:HIS529 3.5 26.3 1.0 OD1 A:ASP564 3.7 36.2 1.0 CD2 A:HIS525 3.9 27.0 1.0 MG A:MG802 4.0 22.8 1.0 CG A:HIS563 4.1 38.1 1.0 ND1 A:HIS563 4.1 38.5 1.0 O A:HOH908 4.2 24.0 1.0 CB A:ASP674 4.3 27.2 1.0 CB A:ASP564 4.3 36.5 1.0 NE2 A:HIS525 4.4 27.1 1.0 CG A:HIS529 4.4 26.6 1.0 ND1 A:HIS529 4.5 26.6 1.0 O A:ASP674 4.6 27.7 1.0 O A:HOH901 4.8 12.9 1.0 CA A:ASP674 4.8 27.8 1.0 CG2 A:VAL533 5.0 27.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE10 in Complex with Inhibitor 2B


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 PDE10 in Complex with Inhibitor 2B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:51.9 occ:1.00 OD2 B:ASP564 2.1 34.7 1.0 OD1 B:ASP674 2.2 31.8 1.0 NE2 B:HIS529 2.3 30.6 1.0 NE2 B:HIS563 2.3 29.2 1.0 CD2 B:HIS529 2.9 30.6 1.0 CG B:ASP674 3.1 31.0 1.0 CG B:ASP564 3.2 34.6 1.0 CE1 B:HIS563 3.2 28.9 1.0 CD2 B:HIS563 3.3 29.4 1.0 OD2 B:ASP674 3.3 31.4 1.0 CE1 B:HIS529 3.4 30.9 1.0 O B:HOH918 3.5 16.9 1.0 OD1 B:ASP564 3.7 34.7 1.0 O B:HOH913 3.8 27.8 1.0 MG B:MG802 3.9 33.3 1.0 CG B:HIS529 4.2 30.7 1.0 CD2 B:HIS525 4.2 40.6 1.0 ND1 B:HIS563 4.3 29.1 1.0 CB B:ASP564 4.3 33.9 1.0 CG B:HIS563 4.4 29.7 1.0 ND1 B:HIS529 4.4 31.0 1.0 CB B:ASP674 4.5 30.3 1.0 CG2 B:VAL533 4.6 29.4 1.0 NE2 B:HIS525 4.6 41.4 1.0 O B:HOH902 4.8 26.6 1.0 CA B:ASP674 4.9 29.9 1.0 O B:ASP674 4.9 30.1 1.0

Y.Y.Huang, Y.F.Yu, C.Zhang, Y.Chen, Q.Zhou, Z.Li, S.Zhou, Z.Li, L.Guo, D.Wu, Y.Wu, H.B.Luo. Validation of Phosphodiesterase-10 As A Novel Target For Pulmonary Arterial Hypertension Via Highly Selective and Subnanomolar Inhibitors. J. Med. Chem. V. 62 3707 2019.
ISSN: ISSN 1520-4804
PubMed: 30888810
DOI: 10.1021/ACS.JMEDCHEM.9B00224