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Magnesium in PDB 5c2a: PDE10 Complexed with 6-Chloro-2-Cyclopropyl-N-[(2,4-Dimethylthiazol-5- Yl)Methyl]-5-Methyl-Pyrimidin-4-Amine

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

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

Protein crystallography data

The structure of PDE10 Complexed with 6-Chloro-2-Cyclopropyl-N-[(2,4-Dimethylthiazol-5- Yl)Methyl]-5-Methyl-Pyrimidin-4-Amine, PDB code: 5c2a was solved by Y.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.73 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.080, 81.340, 158.000, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 23.9

Other elements in 5c2a:

The structure of PDE10 Complexed with 6-Chloro-2-Cyclopropyl-N-[(2,4-Dimethylthiazol-5- Yl)Methyl]-5-Methyl-Pyrimidin-4-Amine also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the PDE10 Complexed with 6-Chloro-2-Cyclopropyl-N-[(2,4-Dimethylthiazol-5- Yl)Methyl]-5-Methyl-Pyrimidin-4-Amine (pdb code 5c2a). 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-N-[(2,4-Dimethylthiazol-5- Yl)Methyl]-5-Methyl-Pyrimidin-4-Amine, PDB code: 5c2a:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5c2a

Go back to Magnesium Binding Sites List in 5c2a
Magnesium binding site 1 out of 2 in the PDE10 Complexed with 6-Chloro-2-Cyclopropyl-N-[(2,4-Dimethylthiazol-5- Yl)Methyl]-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-N-[(2,4-Dimethylthiazol-5- Yl)Methyl]-5-Methyl-Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:30.0
occ:1.00
O A:HOH904 2.0 26.9 1.0
O A:HOH941 2.0 31.0 1.0
OD1 A:ASP554 2.0 30.8 1.0
O A:HOH907 2.1 32.0 1.0
O A:HOH912 2.1 25.5 1.0
O A:HOH959 2.2 34.2 1.0
CG A:ASP554 3.1 33.6 1.0
OD2 A:ASP554 3.5 37.7 1.0
OE2 A:GLU582 3.8 36.1 1.0
ZN A:ZN801 3.8 45.3 1.0
NE2 A:HIS585 3.9 35.4 1.0
OG1 A:THR623 4.1 28.5 1.0
O A:HOH960 4.2 33.6 1.0
CD2 A:HIS585 4.2 36.2 1.0
O A:HOH948 4.3 32.5 1.0
O A:HIS553 4.3 29.1 1.0
CD2 A:HIS553 4.3 28.3 1.0
CD2 A:HIS557 4.4 38.9 1.0
O A:HOH919 4.4 46.1 1.0
CB A:ASP554 4.4 29.1 1.0
OD2 A:ASP664 4.6 32.9 1.0
O A:THR623 4.6 29.9 1.0
NE2 A:HIS557 4.6 38.6 1.0
NE2 A:HIS515 4.7 34.0 1.0
CD A:GLU582 4.7 35.2 1.0
CA A:ASP554 4.7 28.4 1.0
CB A:THR623 4.8 29.7 1.0
NE2 A:HIS553 4.8 28.1 1.0
CD2 A:HIS515 4.8 35.0 1.0
CG A:GLU582 4.8 33.5 1.0

Magnesium binding site 2 out of 2 in 5c2a

Go back to Magnesium Binding Sites List in 5c2a
Magnesium binding site 2 out of 2 in the PDE10 Complexed with 6-Chloro-2-Cyclopropyl-N-[(2,4-Dimethylthiazol-5- Yl)Methyl]-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-N-[(2,4-Dimethylthiazol-5- Yl)Methyl]-5-Methyl-Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:32.0
occ:1.00
O B:HOH923 2.0 32.3 1.0
O B:HOH906 2.0 29.4 1.0
OD1 B:ASP554 2.1 29.8 1.0
O B:HOH939 2.1 38.1 1.0
O B:HOH911 2.1 37.2 1.0
O B:HOH932 2.2 35.8 1.0
CG B:ASP554 3.1 32.0 1.0
OD2 B:ASP554 3.5 32.7 1.0
OE2 B:GLU582 3.8 42.9 1.0
ZN B:ZN801 3.8 55.2 1.0
NE2 B:HIS585 4.1 37.9 1.0
O B:HOH938 4.1 35.4 1.0
OG1 B:THR623 4.2 36.8 1.0
CD2 B:HIS557 4.3 38.6 1.0
CD2 B:HIS553 4.4 37.6 1.0
O B:HOH952 4.4 38.3 1.0
CD2 B:HIS585 4.4 38.4 1.0
O B:HOH942 4.4 39.5 1.0
O B:HIS553 4.4 36.0 1.0
CB B:ASP554 4.4 31.4 1.0
OD2 B:ASP664 4.5 36.2 1.0
O B:THR623 4.5 37.1 1.0
NE2 B:HIS557 4.6 38.2 1.0
NE2 B:HIS515 4.6 39.3 1.0
CB B:THR623 4.7 39.4 1.0
CD2 B:HIS515 4.7 39.8 1.0
NE2 B:HIS553 4.8 37.4 1.0
CD B:GLU582 4.8 53.0 1.0
CA B:ASP554 4.8 30.2 1.0
CG B:GLU582 4.9 46.9 1.0
O B:HOH948 5.0 35.0 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 20:05:17 2020

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