Magnesium in PDB 5c1w: PDE10 Complexed with 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine

All present enzymatic activity of PDE10 Complexed with 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine:
3.1.4.17; 3.1.4.35;

The structure of PDE10 Complexed with 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine, PDB code: 5c1w was solved by Y.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.06 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.430, 81.850, 153.770, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 22.9

The structure of PDE10 Complexed with 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the PDE10 Complexed with 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine (pdb code 5c1w). 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 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine, PDB code: 5c1w:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the PDE10 Complexed with 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine


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 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:20.3 occ:1.00 O A:HOH923 2.0 19.3 1.0 OD1 A:ASP554 2.1 18.4 1.0 O A:HOH911 2.1 18.9 1.0 O A:HOH910 2.1 20.1 1.0 O A:HOH1050 2.2 20.5 1.0 O A:HOH930 2.2 19.5 1.0 CG A:ASP554 3.1 18.9 1.0 OD2 A:ASP554 3.4 18.3 1.0 ZN A:ZN801 3.7 27.0 1.0 OE2 A:GLU582 4.0 32.4 1.0 O A:HOH979 4.0 20.2 1.0 O A:HOH1084 4.0 43.0 1.0 NE2 A:HIS585 4.1 24.7 1.0 OG1 A:THR623 4.1 20.6 1.0 CD2 A:HIS553 4.1 19.3 1.0 O A:HIS553 4.3 21.1 1.0 CD2 A:HIS585 4.3 25.1 1.0 O A:HOH983 4.3 26.6 1.0 OD2 A:ASP664 4.4 29.9 1.0 CB A:ASP554 4.4 16.6 1.0 NE2 A:HIS553 4.5 17.9 1.0 O A:THR623 4.6 21.8 1.0 CD2 A:HIS557 4.6 23.1 1.0 CB A:THR623 4.7 20.2 1.0 CD2 A:HIS515 4.7 25.1 1.0 NE2 A:HIS515 4.7 25.5 1.0 CA A:ASP554 4.8 16.1 1.0 CD A:GLU582 4.8 38.3 1.0 CG A:GLU582 4.8 25.6 1.0 NE2 A:HIS557 4.9 22.7 1.0 OD1 A:ASP664 5.0 17.3 1.0

Magnesium binding site 2 out of 2 in the PDE10 Complexed with 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine


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 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:21.8 occ:1.00 O B:HOH1059 2.0 27.4 1.0 O B:HOH914 2.0 22.6 1.0 O B:HOH985 2.0 26.5 1.0 OD1 B:ASP554 2.1 22.2 1.0 O B:HOH911 2.1 21.5 1.0 O B:HOH917 2.2 25.4 1.0 CG B:ASP554 3.1 26.8 1.0 OD2 B:ASP554 3.4 25.0 1.0 ZN B:ZN801 3.7 31.9 1.0 OE2 B:GLU582 4.0 28.9 1.0 NE2 B:HIS585 4.0 24.2 1.0 OG1 B:THR623 4.1 23.8 1.0 CD2 B:HIS553 4.2 20.5 1.0 CD2 B:HIS557 4.2 30.7 1.0 O B:HOH930 4.2 26.6 1.0 O B:HIS553 4.2 24.3 1.0 CD2 B:HIS585 4.3 23.2 1.0 NE2 B:HIS557 4.4 30.7 1.0 CD2 B:HIS515 4.4 37.6 1.0 O B:THR623 4.4 23.6 1.0 CB B:ASP554 4.5 22.1 1.0 OD2 B:ASP664 4.5 30.4 1.0 NE2 B:HIS553 4.5 20.3 1.0 CB B:THR623 4.6 23.6 1.0 CA B:ASP554 4.8 19.3 1.0 CD B:GLU582 4.9 31.3 1.0 CG B:GLU582 4.9 23.1 1.0 O B:HOH906 5.0 37.1 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