Zinc in PDB 5k9r: PDE10A with Imidazopyrazine Inhibitor

All present enzymatic activity of PDE10A with Imidazopyrazine Inhibitor:
3.1.4.17; 3.1.4.35;

The structure of PDE10A with Imidazopyrazine Inhibitor, PDB code: 5k9r was solved by A.G.Gibbs, C.Schubert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.460, 81.200, 160.150, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 32.2

The structure of PDE10A with Imidazopyrazine Inhibitor also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the PDE10A with Imidazopyrazine Inhibitor (pdb code 5k9r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the PDE10A with Imidazopyrazine Inhibitor, PDB code: 5k9r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the PDE10A with Imidazopyrazine Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PDE10A with Imidazopyrazine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:40.5 occ:1.00 NE2 A:HIS519 2.0 32.8 1.0 OD2 A:ASP554 2.0 38.3 1.0 NE2 A:HIS553 2.1 35.1 1.0 O A:HOH904 2.2 26.8 1.0 OD1 A:ASP664 2.3 29.9 1.0 CE1 A:HIS519 2.9 32.6 1.0 CE1 A:HIS553 3.1 35.4 1.0 CD2 A:HIS519 3.1 34.0 1.0 CD2 A:HIS553 3.1 34.2 1.0 CG A:ASP554 3.2 37.2 1.0 CG A:ASP664 3.2 29.9 1.0 OD2 A:ASP664 3.5 32.8 1.0 OD1 A:ASP554 3.7 35.2 1.0 O A:HOH912 3.8 35.6 1.0 CD2 A:HIS515 4.0 37.6 1.0 ND1 A:HIS519 4.0 33.0 1.0 CG A:HIS519 4.2 33.0 1.0 ND1 A:HIS553 4.2 35.1 1.0 CG A:HIS553 4.3 35.8 1.0 CB A:ASP554 4.4 36.8 1.0 O A:ASP664 4.4 28.8 1.0 NE2 A:HIS515 4.4 37.4 1.0 MG A:MG802 4.5 24.3 1.0 CB A:ASP664 4.6 29.3 1.0 O A:HOH913 4.6 22.0 1.0 CG2 A:VAL523 4.8 32.8 1.0 CA A:ASP664 4.9 29.4 1.0

Zinc binding site 2 out of 2 in the PDE10A with Imidazopyrazine Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of PDE10A with Imidazopyrazine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:43.5 occ:1.00 NE2 B:HIS553 1.9 40.6 1.0 OD2 B:ASP554 2.0 38.9 1.0 O B:HOH903 2.2 5.5 1.0 NE2 B:HIS519 2.3 32.4 1.0 OD2 B:ASP664 2.5 33.5 1.0 CD2 B:HIS553 2.6 40.1 1.0 OD1 B:ASP664 2.6 35.4 1.0 CG B:ASP664 2.9 34.7 1.0 CE1 B:HIS553 3.1 40.7 1.0 CG B:ASP554 3.1 38.8 1.0 CD2 B:HIS519 3.2 33.1 1.0 CE1 B:HIS519 3.3 32.7 1.0 OD1 B:ASP554 3.7 35.8 1.0 MG B:MG802 3.8 28.1 1.0 CG B:HIS553 3.8 39.5 1.0 CD2 B:HIS515 3.9 41.2 1.0 ND1 B:HIS553 4.0 40.3 1.0 NE2 B:HIS515 4.1 41.4 1.0 O B:HOH913 4.2 14.5 1.0 CB B:ASP664 4.3 35.2 1.0 CB B:ASP554 4.3 40.2 1.0 CG B:HIS519 4.3 34.0 1.0 ND1 B:HIS519 4.4 32.5 1.0 O B:HOH912 4.4 18.6 1.0 CG2 B:VAL523 4.6 33.5 1.0 CA B:ASP664 4.7 35.5 1.0 O B:ASP664 4.8 35.7 1.0

S.K.Meegalla, H.Huang, C.R.Illig, D.J.Parks, J.Chen, Y.K.Lee, K.J.Wilson, S.K.Patel, W.S.Cheung, T.Lu, T.Kirchner, H.B.Askari, J.Geisler, R.J.Patch, A.C.Gibbs, B.Rady, M.Connelly, M.R.Player. Discovery of Novel Potent Imidazo[1,2-B]Pyridazine PDE10A Inhibitors. Bioorg.Med.Chem.Lett. V. 26 4216 2016.
ISSN: ESSN 1464-3405
PubMed: 27491708
DOI: 10.1016/J.BMCL.2016.07.054