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Magnesium in PDB 5c2e: PDE10 Complexed WITH6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[2-(2-Pyridyl)Ethoxy]Pyrimidin-4-Amine

Enzymatic activity of PDE10 Complexed WITH6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[2-(2-Pyridyl)Ethoxy]Pyrimidin-4-Amine

All present enzymatic activity of PDE10 Complexed WITH6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[2-(2-Pyridyl)Ethoxy]Pyrimidin-4-Amine:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of PDE10 Complexed WITH6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[2-(2-Pyridyl)Ethoxy]Pyrimidin-4-Amine, PDB code: 5c2e was solved by Y.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.96 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.500, 81.350, 158.400, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 28

Other elements in 5c2e:

The structure of PDE10 Complexed WITH6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[2-(2-Pyridyl)Ethoxy]Pyrimidin-4-Amine also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the PDE10 Complexed WITH6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[2-(2-Pyridyl)Ethoxy]Pyrimidin-4-Amine (pdb code 5c2e). 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 WITH6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[2-(2-Pyridyl)Ethoxy]Pyrimidin-4-Amine, PDB code: 5c2e:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5c2e

Go back to Magnesium Binding Sites List in 5c2e
Magnesium binding site 1 out of 2 in the PDE10 Complexed WITH6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[2-(2-Pyridyl)Ethoxy]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 WITH6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[2-(2-Pyridyl)Ethoxy]Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:29.2
occ:1.00
 O A:HOH903 1.9 28.2 1.0
O A:HOH904 2.0 32.5 1.0
O A:HOH932 2.0 35.1 1.0
O A:HOH908 2.0 27.0 1.0
OD1 A:ASP554 2.1 37.8 1.0
O A:HOH950 2.1 32.0 1.0
CG A:ASP554 2.9 37.4 1.0
OD2 A:ASP554 3.2 38.8 1.0
OE2 A:GLU582 3.8 33.6 1.0
ZN A:ZN801 3.8 44.6 1.0
NE2 A:HIS585 4.0 43.4 1.0
OG1 A:THR623 4.1 28.8 1.0
CD2 A:HIS553 4.1 33.0 1.0
O A:HIS553 4.2 32.1 1.0
O A:HOH939 4.2 36.0 1.0
C12 A:4PX803 4.2 43.8 1.0
CD2 A:HIS585 4.3 43.6 1.0
O A:HOH942 4.3 34.5 1.0
CB A:ASP554 4.3 32.3 1.0
CD2 A:HIS557 4.5 43.8 1.0
OD2 A:ASP664 4.5 42.4 1.0
O A:THR623 4.5 32.6 1.0
NE2 A:HIS553 4.5 32.9 1.0
NE2 A:HIS515 4.7 41.2 1.0
NE2 A:HIS557 4.7 43.4 1.0
CB A:THR623 4.7 28.7 1.0
CD A:GLU582 4.7 45.0 1.0
CD2 A:HIS515 4.7 41.5 1.0
CA A:ASP554 4.8 31.2 1.0
CG A:GLU582 4.8 41.4 1.0
C11 A:4PX803 4.8 44.6 1.0
C A:HIS553 5.0 33.2 1.0

Magnesium binding site 2 out of 2 in 5c2e

Go back to Magnesium Binding Sites List in 5c2e
Magnesium binding site 2 out of 2 in the PDE10 Complexed WITH6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[2-(2-Pyridyl)Ethoxy]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 WITH6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[2-(2-Pyridyl)Ethoxy]Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:43.0
occ:1.00
 O B:HOH918 1.9 34.0 1.0
O B:HOH939 1.9 33.3 1.0
O B:HOH905 2.1 36.1 1.0
O B:HOH928 2.1 36.5 1.0
OD1 B:ASP554 2.1 40.6 1.0
O B:HOH906 2.2 34.6 1.0
CG B:ASP554 3.2 40.8 1.0
OD2 B:ASP554 3.6 44.5 1.0
ZN B:ZN801 3.8 60.1 1.0
OE2 B:GLU582 4.0 41.4 1.0
NE2 B:HIS585 4.0 47.0 1.0
O B:HOH926 4.0 33.2 1.0
OG1 B:THR623 4.2 46.1 1.0
O B:HOH921 4.3 41.2 1.0
O B:HIS553 4.3 38.8 1.0
O B:HOH923 4.3 53.3 1.0
CD2 B:HIS557 4.4 43.4 1.0
CD2 B:HIS585 4.4 47.3 1.0
OD2 B:ASP664 4.4 36.6 1.0
NE2 B:HIS557 4.5 43.3 1.0
NE2 B:HIS515 4.5 38.5 1.0
CB B:ASP554 4.5 35.3 1.0
CD2 B:HIS553 4.5 40.7 1.0
O B:THR623 4.6 43.9 1.0
CD2 B:HIS515 4.6 38.7 1.0
CB B:THR623 4.6 45.8 1.0
CA B:ASP554 4.9 34.2 1.0
NE2 B:HIS553 4.9 40.5 1.0
O B:HOH943 5.0 42.3 1.0
CD B:GLU582 5.0 54.6 1.0

Reference:

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
Page generated: Tue Aug 12 06:14:18 2025

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