Zinc 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:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5c2e

Go back to Zinc Binding Sites List in 5c2e
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:44.6
occ:1.00
 OD1 A:ASP664 2.0 37.4 1.0
OD2 A:ASP554 2.1 38.8 1.0
NE2 A:HIS553 2.1 32.9 1.0
NE2 A:HIS519 2.1 33.8 1.0
O A:HOH939 2.2 36.0 1.0
O A:HOH903 2.3 28.2 1.0
CG A:ASP664 2.9 37.6 1.0
CD2 A:HIS553 3.0 33.0 1.0
CD2 A:HIS519 3.1 34.3 1.0
CE1 A:HIS519 3.1 33.5 1.0
CE1 A:HIS553 3.1 32.7 1.0
OD2 A:ASP664 3.2 42.4 1.0
CG A:ASP554 3.2 37.4 1.0
MG A:MG802 3.8 29.2 1.0
OD1 A:ASP554 3.9 37.8 1.0
CD2 A:HIS515 4.0 41.5 1.0
O A:HOH950 4.1 32.0 1.0
O A:HOH901 4.1 28.7 1.0
CG A:HIS553 4.2 31.9 1.0
ND1 A:HIS553 4.2 33.5 1.0
CG A:HIS519 4.2 33.0 1.0
ND1 A:HIS519 4.3 34.3 1.0
CB A:ASP664 4.3 29.9 1.0
NE2 A:HIS515 4.3 41.2 1.0
CB A:ASP554 4.3 32.3 1.0
CG2 A:VAL523 4.7 30.3 1.0
O A:HOH904 4.7 32.5 1.0
C12 A:4PX803 4.7 43.8 1.0
CA A:ASP664 4.7 28.1 1.0
O A:ASP664 4.9 29.9 1.0
O A:HOH908 4.9 27.0 1.0

Zinc binding site 2 out of 2 in 5c2e

Go back to Zinc Binding Sites List in 5c2e
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:60.1
occ:1.00
 OD1 B:ASP664 2.0 36.5 1.0
OD2 B:ASP554 2.1 44.5 1.0
O B:HOH918 2.1 34.0 1.0
NE2 B:HIS553 2.2 40.5 1.0
NE2 B:HIS519 2.3 35.1 1.0
O B:HOH923 2.8 53.3 1.0
CG B:ASP664 2.9 36.8 1.0
CD2 B:HIS553 3.0 40.7 1.0
CD2 B:HIS519 3.1 35.3 1.0
OD2 B:ASP664 3.1 36.6 1.0
CG B:ASP554 3.1 40.8 1.0
CE1 B:HIS553 3.3 40.1 1.0
CE1 B:HIS519 3.4 35.0 1.0
OD1 B:ASP554 3.6 40.6 1.0
CD2 B:HIS515 3.7 38.7 1.0
MG B:MG802 3.8 43.0 1.0
O B:HOH928 4.0 36.5 1.0
NE2 B:HIS515 4.0 38.5 1.0
CG B:HIS553 4.2 39.0 1.0
CB B:ASP664 4.3 34.3 1.0
CG B:HIS519 4.3 34.3 1.0
ND1 B:HIS553 4.3 40.8 1.0
CB B:ASP554 4.4 35.3 1.0
ND1 B:HIS519 4.4 35.8 1.0
O B:HOH912 4.5 38.3 1.0
O B:HOH905 4.6 36.1 1.0
O B:HOH921 4.6 41.2 1.0
CG2 B:VAL523 4.7 39.8 1.0
CA B:ASP664 4.7 33.0 1.0
O B:ASP664 4.8 36.7 1.0
CG B:HIS515 5.0 37.1 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: Wed Dec 16 06:05:50 2020

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