Magnesium 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:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-Pyrimidin-4-Amine, PDB code: 5c28:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802 b:12.7 occ:1.00 O A:HOH935 2.1 13.9 1.0 O A:HOH920 2.1 14.9 1.0 OD1 A:ASP554 2.1 13.1 1.0 O A:HOH1072 2.1 14.4 1.0 O A:HOH955 2.1 12.9 1.0 O A:HOH916 2.1 11.7 1.0 CG A:ASP554 3.1 14.2 1.0 OD2 A:ASP554 3.5 13.6 1.0 ZN A:ZN801 3.7 19.0 1.0 O A:HOH1099 3.9 28.8 1.0 OE2 A:GLU582 4.0 18.0 1.0 NE2 A:HIS585 4.0 13.2 1.0 O A:HOH990 4.1 15.9 1.0 OG1 A:THR623 4.2 13.4 1.0 CD2 A:HIS553 4.2 13.5 1.0 O A:HOH1029 4.3 18.1 1.0 CD2 A:HIS585 4.3 13.2 1.0 O A:HIS553 4.3 12.9 1.0 CB A:ASP554 4.5 10.4 1.0 OD2 A:ASP664 4.5 23.2 1.0 CD2 A:HIS557 4.6 14.6 1.0 NE2 A:HIS553 4.6 11.6 1.0 O A:THR623 4.6 15.3 1.0 NE2 A:HIS515 4.6 16.6 1.0 CD2 A:HIS515 4.6 16.5 1.0 CB A:THR623 4.7 12.5 1.0 CG A:GLU582 4.8 14.7 1.0 CD A:GLU582 4.8 21.2 1.0 CA A:ASP554 4.8 10.3 1.0 NE2 A:HIS557 4.9 14.2 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802 b:15.9 occ:1.00 O B:HOH1130 2.1 17.8 1.0 OD1 B:ASP554 2.1 13.6 1.0 O B:HOH914 2.1 16.8 1.0 O B:HOH927 2.1 13.8 1.0 O B:HOH1008 2.1 15.7 1.0 O B:HOH980 2.1 18.4 1.0 CG B:ASP554 3.1 16.2 1.0 OD2 B:ASP554 3.5 21.6 1.0 ZN B:ZN801 3.7 24.4 1.0 O B:HOH945 3.9 52.6 1.0 OE2 B:GLU582 4.0 21.2 1.0 NE2 B:HIS585 4.0 15.9 1.0 O B:HOH1099 4.1 28.1 1.0 OG1 B:THR623 4.1 15.6 1.0 CD2 B:HIS553 4.2 15.4 1.0 O B:HIS553 4.3 14.7 1.0 CD2 B:HIS585 4.3 16.4 1.0 CB B:ASP554 4.4 13.2 1.0 O B:THR623 4.5 17.0 1.0 CD2 B:HIS557 4.5 23.1 1.0 NE2 B:HIS553 4.6 14.8 1.0 CD2 B:HIS515 4.6 28.6 1.0 CB B:THR623 4.7 14.7 1.0 OD2 B:ASP664 4.7 21.5 1.0 O B:HOH901 4.7 20.5 1.0 CA B:ASP554 4.8 10.9 1.0 CG B:GLU582 4.9 17.3 1.0 O B:HOH1116 4.9 24.4 1.0 CD B:GLU582 4.9 23.6 1.0 NE2 B:HIS557 4.9 23.7 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