Zinc in PDB 4xy2: Crystal Structure of PDE10A in Complex with ASP9436

All present enzymatic activity of Crystal Structure of PDE10A in Complex with ASP9436:
3.1.4.17; 3.1.4.35;

The structure of Crystal Structure of PDE10A in Complex with ASP9436, PDB code: 4xy2 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)	79.57 / 2.03
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.447, 82.114, 159.150, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 26

The structure of Crystal Structure of PDE10A in Complex with ASP9436 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 ASP9436 (pdb code 4xy2). 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 ASP9436, PDB code: 4xy2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PDE10A in Complex with ASP9436


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 ASP9436 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:31.7 occ:1.00 O A:HOH928 1.8 19.7 1.0 NE2 A:HIS563 2.2 24.3 1.0 NE2 A:HIS529 2.2 22.5 1.0 OD1 A:ASP674 2.2 23.7 1.0 OD2 A:ASP564 2.3 26.9 1.0 O A:HOH922 2.5 24.9 1.0 CD2 A:HIS563 2.9 23.4 1.0 CG A:ASP674 3.1 23.8 1.0 CE1 A:HIS529 3.1 26.4 1.0 CG A:ASP564 3.2 25.5 1.0 CD2 A:HIS529 3.2 23.7 1.0 CE1 A:HIS563 3.3 23.2 1.0 OD2 A:ASP674 3.4 27.3 1.0 O A:HOH924 3.4 20.6 1.0 OD1 A:ASP564 3.6 29.2 1.0 O A:HOH925 3.7 27.3 1.0 MG A:MG802 3.7 25.0 1.0 O A:HOH970 4.0 38.7 1.0 CG A:HIS563 4.2 24.8 1.0 ND1 A:HIS529 4.3 24.1 1.0 CB A:ASP564 4.3 23.4 1.0 ND1 A:HIS563 4.3 25.0 1.0 CG A:HIS529 4.4 23.3 1.0 CB A:ASP674 4.5 21.8 1.0 CD2 A:HIS525 4.5 31.2 1.0 O A:HOH921 4.5 23.7 1.0 O A:HOH960 4.8 24.1 1.0 O A:ASP674 4.9 24.7 1.0 CG2 A:VAL533 4.9 22.7 1.0 CA A:ASP674 4.9 21.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE10A in Complex with ASP9436


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 ASP9436 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:26.0 occ:1.00 O B:HOH923 1.9 22.0 1.0 NE2 B:HIS529 2.1 18.5 1.0 NE2 B:HIS563 2.2 21.2 1.0 OD2 B:ASP564 2.2 19.1 1.0 OD1 B:ASP674 2.2 19.4 1.0 O B:HOH924 2.3 32.8 1.0 CD2 B:HIS529 3.1 19.6 1.0 CG B:ASP674 3.1 23.7 1.0 CG B:ASP564 3.1 24.4 1.0 CE1 B:HIS529 3.1 19.2 1.0 CE1 B:HIS563 3.1 24.2 1.0 CD2 B:HIS563 3.2 20.2 1.0 OD2 B:ASP674 3.4 24.5 1.0 OD1 B:ASP564 3.4 26.7 1.0 MG B:MG802 3.6 24.0 1.0 O B:HOH917 3.7 30.9 1.0 O B:HOH918 4.0 29.9 1.0 ND1 B:HIS529 4.2 19.1 1.0 CG B:HIS529 4.2 20.3 1.0 ND1 B:HIS563 4.3 21.9 1.0 CG B:HIS563 4.3 20.1 1.0 CD2 B:HIS525 4.3 24.2 1.0 O B:HOH940 4.4 27.3 1.0 CB B:ASP564 4.4 23.0 1.0 CB B:ASP674 4.5 21.8 1.0 O B:HOH919 4.6 36.0 1.0 O B:ASP674 4.8 20.5 1.0 O B:HOH921 4.8 22.0 1.0 NE2 B:HIS525 4.8 24.0 1.0 CG2 B:VAL533 4.9 17.9 1.0 CA B:ASP674 4.9 21.3 1.0

W.Hamaguchi, N.Masuda, S.Miyamoto, S.Kikuchi, F.Narazaki, Y.Shiina, R.Seo, Y.Amano, T.Mihara, H.Moriguchi, K.Hattori. Addressing Phototoxicity Observed in A Novel Series of Biaryl Derivatives: Discovery of Potent, Selective and Orally Active Phosphodiesterase 10A Inhibitor ASP9436 Bioorg.Med.Chem. V. 23 3351 2015.
ISSN: ESSN 1464-3391
PubMed: 25960322
DOI: 10.1016/J.BMC.2015.04.052