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Zinc 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:

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

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 5c2h

Go back to Zinc Binding Sites List in 5c2h
Zinc 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 Zinc with other atoms in the Zn 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:Zn901

b:44.2
occ:1.00
OD2 A:ASP554 2.0 34.6 1.0
NE2 A:HIS519 2.2 31.0 1.0
NE2 A:HIS553 2.2 32.4 1.0
OD1 A:ASP664 2.2 27.1 1.0
O A:HOH1006 2.3 37.7 1.0
O A:HOH1016 2.5 23.3 1.0
CD2 A:HIS553 2.9 32.4 1.0
CG A:ASP554 3.0 35.2 1.0
CD2 A:HIS519 3.1 31.6 1.0
CG A:ASP664 3.1 29.8 1.0
CE1 A:HIS519 3.2 30.1 1.0
CE1 A:HIS553 3.3 33.1 1.0
OD2 A:ASP664 3.3 31.6 1.0
OD1 A:ASP554 3.6 33.0 1.0
CD2 A:HIS515 3.9 36.5 1.0
MG A:MG902 4.0 27.6 1.0
O A:HOH1027 4.1 29.9 1.0
CG A:HIS553 4.1 32.3 1.0
NE2 A:HIS515 4.2 35.8 1.0
CB A:ASP554 4.2 31.6 1.0
O A:HOH1010 4.2 30.0 1.0
CG A:HIS519 4.2 29.0 1.0
ND1 A:HIS553 4.3 33.7 1.0
ND1 A:HIS519 4.3 29.5 1.0
CB A:ASP664 4.5 25.6 1.0
O A:HOH1001 4.6 32.4 1.0
CG2 A:VAL523 4.7 33.0 1.0
CA A:ASP664 4.9 23.8 1.0
C12 A:4PX903 4.9 27.0 1.0
O A:ASP664 4.9 29.2 1.0

Zinc binding site 2 out of 2 in 5c2h

Go back to Zinc Binding Sites List in 5c2h
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:52.1
occ:1.00
OD2 B:ASP554 2.1 36.9 1.0
NE2 B:HIS519 2.1 28.9 1.0
OD1 B:ASP664 2.2 25.2 1.0
NE2 B:HIS553 2.3 31.5 1.0
O B:HOH910 2.3 34.2 1.0
CD2 B:HIS553 3.0 31.9 1.0
CD2 B:HIS519 3.0 29.3 1.0
CG B:ASP664 3.1 26.8 1.0
CG B:ASP554 3.1 37.5 1.0
CE1 B:HIS519 3.2 29.1 1.0
OD2 B:ASP664 3.3 31.4 1.0
CE1 B:HIS553 3.4 31.1 1.0
OD1 B:ASP554 3.7 38.0 1.0
CD2 B:HIS515 3.8 42.1 1.0
MG B:MG802 3.9 40.9 1.0
NE2 B:HIS515 4.1 42.1 1.0
O B:HOH913 4.1 33.7 1.0
CG B:HIS519 4.2 28.5 1.0
CG B:HIS553 4.2 30.9 1.0
ND1 B:HIS519 4.3 30.2 1.0
CB B:ASP554 4.3 30.1 1.0
O B:HOH906 4.4 46.0 1.0
ND1 B:HIS553 4.4 32.2 1.0
CB B:ASP664 4.5 24.4 1.0
O B:HOH903 4.6 33.4 1.0
CG2 B:VAL523 4.7 27.5 1.0
O B:ASP664 4.8 32.1 1.0
CA B:ASP664 4.8 24.1 1.0
O B:HOH905 5.0 38.4 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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