Zinc in PDB 6ijh: Crystal Structure of PDE10 in Complex with Inhibitor Af-399/14387019

All present enzymatic activity of Crystal Structure of PDE10 in Complex with Inhibitor Af-399/14387019:
3.1.4.17; 3.1.4.35;

The structure of Crystal Structure of PDE10 in Complex with Inhibitor Af-399/14387019, PDB code: 6ijh 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)	79.91 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.342, 81.693, 159.816, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 31.2

The structure of Crystal Structure of PDE10 in Complex with Inhibitor Af-399/14387019 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 Af-399/14387019 (pdb code 6ijh). 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 Af-399/14387019, PDB code: 6ijh:
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 Af-399/14387019


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 Af-399/14387019 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:31.7 occ:1.00 OD2 A:ASP564 2.0 24.7 1.0 OD1 A:ASP674 2.2 18.4 1.0 NE2 A:HIS563 2.2 23.6 1.0 O A:HOH907 2.4 8.8 1.0 NE2 A:HIS529 2.4 19.4 1.0 CD2 A:HIS563 2.9 23.6 1.0 CG A:ASP674 3.0 18.9 1.0 CG A:ASP564 3.0 24.0 1.0 OD2 A:ASP674 3.1 18.2 1.0 CD2 A:HIS529 3.3 19.2 1.0 CE1 A:HIS563 3.4 23.5 1.0 CE1 A:HIS529 3.4 19.5 1.0 OD1 A:ASP564 3.5 23.8 1.0 O A:HOH908 3.6 42.0 1.0 MG A:MG802 3.8 21.4 1.0 CD2 A:HIS525 3.9 23.6 1.0 CG A:HIS563 4.2 23.4 1.0 NE2 A:HIS525 4.3 23.6 1.0 CB A:ASP564 4.3 23.9 1.0 ND1 A:HIS563 4.3 23.8 1.0 O A:HOH902 4.4 18.9 1.0 CG A:HIS529 4.5 19.4 1.0 CB A:ASP674 4.5 19.4 1.0 ND1 A:HIS529 4.5 19.5 1.0 O A:HOH901 4.9 5.3 1.0 O A:HOH910 4.9 15.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE10 in Complex with Inhibitor Af-399/14387019


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 Af-399/14387019 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:51.7 occ:1.00 O B:HOH919 2.0 16.9 1.0 OD2 B:ASP564 2.2 22.6 1.0 NE2 B:HIS563 2.2 19.9 1.0 NE2 B:HIS529 2.2 27.7 1.0 OD1 B:ASP674 2.3 21.8 1.0 CD2 B:HIS529 3.0 27.1 1.0 CD2 B:HIS563 3.1 20.1 1.0 CG B:ASP564 3.2 22.4 1.0 CE1 B:HIS563 3.3 20.1 1.0 CE1 B:HIS529 3.3 27.6 1.0 CG B:ASP674 3.4 21.9 1.0 OD1 B:ASP564 3.7 21.8 1.0 MG B:MG802 3.9 13.6 1.0 O B:HOH903 3.9 18.6 1.0 OD2 B:ASP674 3.9 22.3 1.0 O B:HOH922 4.0 8.1 1.0 CG B:HIS529 4.2 27.0 1.0 CD2 B:HIS525 4.2 31.9 1.0 CG B:HIS563 4.3 20.5 1.0 O B:HOH911 4.3 22.3 1.0 ND1 B:HIS563 4.3 20.1 1.0 ND1 B:HIS529 4.3 27.7 1.0 CB B:ASP564 4.4 22.4 1.0 CB B:ASP674 4.5 21.9 1.0 CG2 B:VAL533 4.5 22.5 1.0 O B:HOH909 4.6 10.9 1.0 NE2 B:HIS525 4.7 32.1 1.0 CA B:ASP674 4.8 21.6 1.0 O B:ASP674 4.9 21.5 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