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Magnesium in PDB 5c2h: PDE10 Complexed with 6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[3-(2-Quinolyl)Propoxy]Pyrimidin-4-Amine

Enzymatic activity of PDE10 Complexed with 6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[3-(2-Quinolyl)Propoxy]Pyrimidin-4-Amine

All present enzymatic activity of PDE10 Complexed with 6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[3-(2-Quinolyl)Propoxy]Pyrimidin-4-Amine:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of PDE10 Complexed with 6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[3-(2-Quinolyl)Propoxy]Pyrimidin-4-Amine, PDB code: 5c2h was solved by Y.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.10 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.657, 81.280, 157.101, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24

Other elements in 5c2h:

The structure of PDE10 Complexed with 6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[3-(2-Quinolyl)Propoxy]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 with 6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[3-(2-Quinolyl)Propoxy]Pyrimidin-4-Amine (pdb code 5c2h). 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-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[3-(2-Quinolyl)Propoxy]Pyrimidin-4-Amine, PDB code: 5c2h:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5c2h

Go back to Magnesium Binding Sites List in 5c2h
Magnesium binding site 1 out of 2 in the PDE10 Complexed with 6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[3-(2-Quinolyl)Propoxy]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-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[3-(2-Quinolyl)Propoxy]Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:27.6
occ:1.00
 O A:HOH1030 1.9 23.1 1.0
O A:HOH1016 1.9 23.3 1.0
O A:HOH1027 2.1 29.9 1.0
O A:HOH1001 2.1 32.4 1.0
OD1 A:ASP554 2.1 33.0 1.0
O A:HOH1002 2.1 25.6 1.0
CG A:ASP554 3.2 35.2 1.0
OD2 A:ASP554 3.5 34.6 1.0
OE2 A:GLU582 3.6 44.7 1.0
NE2 A:HIS585 3.9 44.8 1.0
ZN A:ZN901 4.0 44.2 1.0
O A:HOH1031 4.0 31.1 1.0
CD2 A:HIS585 4.1 45.1 1.0
OG1 A:THR623 4.1 28.6 1.0
O A:HIS553 4.2 38.0 1.0
CD2 A:HIS557 4.3 46.2 1.0
O A:HOH1006 4.3 37.7 1.0
C12 A:4PX903 4.3 27.0 1.0
CB A:ASP554 4.5 31.6 1.0
O A:THR623 4.5 33.6 1.0
CD2 A:HIS553 4.5 32.4 1.0
NE2 A:HIS557 4.5 45.9 1.0
OD2 A:ASP664 4.5 31.6 1.0
CD A:GLU582 4.6 49.3 1.0
NE2 A:HIS515 4.6 35.8 1.0
CG A:GLU582 4.7 47.4 1.0
CD2 A:HIS515 4.7 36.5 1.0
CA A:ASP554 4.8 30.4 1.0
CB A:THR623 4.8 29.4 1.0
C11 A:4PX903 4.8 32.3 1.0
O A:HOH1033 4.9 37.3 1.0

Magnesium binding site 2 out of 2 in 5c2h

Go back to Magnesium Binding Sites List in 5c2h
Magnesium binding site 2 out of 2 in the PDE10 Complexed with 6-Chloro-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[3-(2-Quinolyl)Propoxy]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-N-[(2,4-Dimethylthiazol-5-Yl)Methyl]-5- Methyl-2-[3-(2-Quinolyl)Propoxy]Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:40.9
occ:1.00
 O B:HOH905 1.9 38.4 1.0
O B:HOH910 2.0 34.2 1.0
OD1 B:ASP554 2.0 38.0 1.0
O B:HOH903 2.0 33.4 1.0
O B:HOH918 2.1 32.7 1.0
O B:HOH913 2.2 33.7 1.0
CG B:ASP554 3.1 37.5 1.0
OD2 B:ASP554 3.5 36.9 1.0
OE2 B:GLU582 3.7 44.9 1.0
ZN B:ZN801 3.9 52.1 1.0
NE2 B:HIS585 4.0 41.9 1.0
O B:HOH916 4.1 30.6 1.0
OG1 B:THR623 4.2 32.1 1.0
CD2 B:HIS585 4.2 42.2 1.0
CD2 B:HIS557 4.3 40.2 1.0
O B:HIS553 4.3 34.2 1.0
CB B:ASP554 4.4 30.1 1.0
O B:THR623 4.5 37.8 1.0
NE2 B:HIS515 4.5 42.1 1.0
NE2 B:HIS557 4.5 40.1 1.0
CD2 B:HIS553 4.5 31.9 1.0
CD2 B:HIS515 4.5 42.1 1.0
OD2 B:ASP664 4.6 31.4 1.0
CD B:GLU582 4.7 58.3 1.0
CA B:ASP554 4.7 28.1 1.0
CG B:GLU582 4.8 50.1 1.0
CB B:THR623 4.8 38.8 1.0
NE2 B:HIS553 5.0 31.5 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: Mon Dec 14 20:05:20 2020

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