Zinc in PDB 5c28: PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-Pyrimidin-4-Amine

All present enzymatic activity of PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-Pyrimidin-4-Amine:
3.1.4.17; 3.1.4.35;

The structure of PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-Pyrimidin-4-Amine, PDB code: 5c28 was solved by Y.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.84 / 1.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.650, 82.040, 152.860, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 19.6

The structure of PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-Pyrimidin-4-Amine also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-Pyrimidin-4-Amine (pdb code 5c28). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-Pyrimidin-4-Amine, PDB code: 5c28:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-Pyrimidin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:19.0 occ:1.00 O A:HOH935 2.0 13.9 1.0 OD2 A:ASP554 2.1 13.6 1.0 OD1 A:ASP664 2.1 13.3 1.0 NE2 A:HIS553 2.1 11.6 1.0 O A:HOH990 2.2 15.9 1.0 NE2 A:HIS519 2.2 12.5 1.0 CD2 A:HIS553 3.0 13.5 1.0 CG A:ASP664 3.0 18.4 1.0 CG A:ASP554 3.1 14.2 1.0 CD2 A:HIS519 3.1 12.1 1.0 CE1 A:HIS519 3.2 12.0 1.0 CE1 A:HIS553 3.2 12.2 1.0 OD2 A:ASP664 3.3 23.2 1.0 OD1 A:ASP554 3.6 13.1 1.0 MG A:MG802 3.7 12.7 1.0 CD2 A:HIS515 4.0 16.5 1.0 O A:HOH1072 4.0 14.4 1.0 CG A:HIS553 4.2 12.7 1.0 O A:HOH1013 4.3 20.7 1.0 CG A:HIS519 4.3 10.6 1.0 ND1 A:HIS553 4.3 13.0 1.0 CB A:ASP554 4.3 10.4 1.0 NE2 A:HIS515 4.4 16.6 1.0 CB A:ASP664 4.4 10.9 1.0 ND1 A:HIS519 4.4 11.8 1.0 O A:HOH1099 4.6 28.8 1.0 O A:HOH916 4.7 11.7 1.0 CG2 A:VAL523 4.8 11.6 1.0 CA A:ASP664 4.8 9.8 1.0 O A:ASP664 4.9 12.8 1.0 O A:HOH920 5.0 14.9 1.0

Zinc binding site 2 out of 2 in the PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-Pyrimidin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:24.4 occ:1.00 O B:HOH901 2.1 20.5 1.0 OD2 B:ASP554 2.1 21.6 1.0 NE2 B:HIS553 2.1 14.8 1.0 O B:HOH1008 2.2 15.7 1.0 NE2 B:HIS519 2.2 19.4 1.0 OD1 B:ASP664 2.2 17.5 1.0 CD2 B:HIS553 3.0 15.4 1.0 CD2 B:HIS519 3.1 19.0 1.0 CG B:ASP664 3.1 19.6 1.0 CG B:ASP554 3.2 16.2 1.0 CE1 B:HIS553 3.2 15.3 1.0 CE1 B:HIS519 3.3 18.2 1.0 OD2 B:ASP664 3.4 21.5 1.0 OD1 B:ASP554 3.6 13.6 1.0 O B:HOH945 3.6 52.6 1.0 MG B:MG802 3.7 15.9 1.0 O B:HOH1130 3.8 17.8 1.0 CG B:HIS553 4.2 14.0 1.0 CG B:HIS519 4.3 16.6 1.0 O B:HOH912 4.3 22.2 1.0 ND1 B:HIS553 4.3 14.9 1.0 ND1 B:HIS519 4.4 19.0 1.0 CB B:ASP554 4.4 13.2 1.0 CB B:ASP664 4.5 12.0 1.0 CD2 B:HIS515 4.7 28.6 1.0 O B:HOH927 4.7 13.8 1.0 CG2 B:VAL523 4.8 13.1 1.0 O B:TYR514 4.8 28.2 1.0 CA B:ASP664 5.0 10.6 1.0

W.D.Shipe, S.S.Sharik, J.C.Barrow, G.B.Mcgaughey, C.R.Theberge, J.M.Uslaner, Y.Yan, J.J.Renger, S.M.Smith, P.J.Coleman, C.D.Cox. Discovery and Optimization of A Series of Pyrimidine-Based Phosphodiesterase 10A (PDE10A) Inhibitors Through Fragment Screening, Structure-Based Design, and Parallel Synthesis. J.Med.Chem. V. 58 7888 2015.
ISSN: ISSN 0022-2623
PubMed: 26378882
DOI: 10.1021/ACS.JMEDCHEM.5B00983