Magnesium in PDB 5c29: PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-N-Propyl- Pyrimidin-4-Amine

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

The structure of PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-N-Propyl- Pyrimidin-4-Amine, PDB code: 5c29 was solved by Y.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.18 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.480, 81.190, 152.990, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 23.4

The structure of PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-N-Propyl- 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-N-Propyl- Pyrimidin-4-Amine (pdb code 5c29). 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-N-Propyl- Pyrimidin-4-Amine, PDB code: 5c29:
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-N-Propyl- 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-N-Propyl- Pyrimidin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:27.6 occ:1.00 O A:HOH901 1.9 26.8 1.0 O A:HOH959 2.0 28.6 1.0 OD1 A:ASP554 2.0 32.8 1.0 O A:HOH914 2.1 23.6 1.0 O A:HOH973 2.1 28.3 1.0 O A:HOH902 2.1 25.2 1.0 CG A:ASP554 3.1 33.8 1.0 OD2 A:ASP554 3.4 29.7 1.0 ZN A:ZN801 3.6 40.4 1.0 OE2 A:GLU582 3.9 45.6 1.0 NE2 A:HIS585 4.0 38.6 1.0 OG1 A:THR623 4.1 24.8 1.0 CD2 A:HIS553 4.2 32.0 1.0 O A:HOH1019 4.2 41.1 1.0 O A:HOH968 4.2 25.8 1.0 CD2 A:HIS585 4.2 38.8 1.0 O A:HIS553 4.3 31.5 1.0 O A:HOH964 4.3 31.7 1.0 OD2 A:ASP664 4.4 40.9 1.0 CB A:ASP554 4.4 28.8 1.0 NE2 A:HIS515 4.5 29.5 1.0 CD2 A:HIS515 4.6 29.6 1.0 CD2 A:HIS557 4.6 35.0 1.0 O A:THR623 4.6 31.8 1.0 NE2 A:HIS553 4.6 31.5 1.0 CA A:ASP554 4.7 28.4 1.0 CB A:THR623 4.8 31.3 1.0 CD A:GLU582 4.8 55.7 1.0 NE2 A:HIS557 4.9 34.1 1.0 CG A:GLU582 5.0 43.6 1.0

Magnesium binding site 2 out of 2 in the PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-N-Propyl- 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-N-Propyl- Pyrimidin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:43.9 occ:1.00 O B:HOH931 1.9 42.6 1.0 O B:HOH989 2.1 34.2 1.0 OD1 B:ASP554 2.1 36.9 1.0 O B:HOH907 2.1 38.0 1.0 O B:HOH905 2.2 40.6 1.0 O B:HOH904 2.2 41.9 1.0 CG B:ASP554 3.2 36.4 1.0 OD2 B:ASP554 3.6 44.3 1.0 ZN B:ZN801 3.7 49.3 1.0 OE2 B:GLU582 3.9 46.9 1.0 NE2 B:HIS585 4.0 53.5 1.0 OG1 B:THR623 4.2 39.4 1.0 CD2 B:HIS585 4.3 53.5 1.0 CD2 B:HIS553 4.4 34.3 1.0 CD2 B:HIS557 4.4 61.4 1.0 O B:THR623 4.4 35.0 1.0 O B:HIS553 4.4 37.9 1.0 CB B:ASP554 4.5 34.3 1.0 O B:HOH974 4.5 31.7 1.0 OD2 B:ASP664 4.5 35.3 1.0 NE2 B:HIS557 4.7 61.2 1.0 CD2 B:HIS515 4.7 60.9 1.0 CB B:THR623 4.8 38.7 1.0 CA B:ASP554 4.8 33.8 1.0 NE2 B:HIS553 4.8 34.2 1.0 CD B:GLU582 4.8 63.2 1.0 O B:HOH901 4.9 42.7 1.0 O B:HOH949 5.0 45.6 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