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Zinc 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:

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

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 5c2a

Go back to Zinc Binding Sites List in 5c2a
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:45.3
occ:1.00
 O A:HOH912 2.1 25.5 1.0
OD2 A:ASP554 2.1 37.7 1.0
OD1 A:ASP664 2.1 32.0 1.0
NE2 A:HIS553 2.2 28.1 1.0
NE2 A:HIS519 2.2 29.8 1.0
O A:HOH919 2.9 46.1 1.0
CG A:ASP664 3.0 31.1 1.0
CD2 A:HIS553 3.0 28.3 1.0
CG A:ASP554 3.1 33.6 1.0
CD2 A:HIS519 3.2 30.3 1.0
OD2 A:ASP664 3.2 32.9 1.0
CE1 A:HIS519 3.3 29.0 1.0
CE1 A:HIS553 3.3 28.4 1.0
OD1 A:ASP554 3.5 30.8 1.0
MG A:MG802 3.8 30.0 1.0
CD2 A:HIS515 3.9 35.0 1.0
O A:HOH959 4.1 34.2 1.0
NE2 A:HIS515 4.2 34.0 1.0
CG A:HIS553 4.2 28.2 1.0
CG A:HIS519 4.3 28.5 1.0
CB A:ASP664 4.4 27.3 1.0
CB A:ASP554 4.4 29.1 1.0
ND1 A:HIS553 4.4 29.4 1.0
O A:HOH902 4.4 29.1 1.0
ND1 A:HIS519 4.4 29.9 1.0
O A:HOH960 4.6 33.6 1.0
O A:HOH907 4.6 32.0 1.0
CA A:ASP664 4.8 24.2 1.0
CG2 A:VAL523 4.9 26.2 1.0
O A:HOH904 4.9 26.9 1.0
O A:ASP664 4.9 26.7 1.0

Zinc binding site 2 out of 2 in 5c2a

Go back to Zinc Binding Sites List in 5c2a
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:55.2
occ:1.00
 OD1 B:ASP664 2.0 35.9 1.0
OD2 B:ASP554 2.1 32.7 1.0
NE2 B:HIS519 2.2 33.9 1.0
O B:HOH923 2.2 32.3 1.0
NE2 B:HIS553 2.3 37.4 1.0
O B:HOH942 2.9 39.5 1.0
CG B:ASP664 2.9 33.6 1.0
CD2 B:HIS519 3.1 34.2 1.0
CD2 B:HIS553 3.1 37.6 1.0
OD2 B:ASP664 3.2 36.2 1.0
CG B:ASP554 3.2 32.0 1.0
CE1 B:HIS519 3.2 33.4 1.0
CE1 B:HIS553 3.4 37.3 1.0
OD1 B:ASP554 3.6 29.8 1.0
MG B:MG802 3.8 32.0 1.0
CD2 B:HIS515 3.8 39.8 1.0
O B:HOH939 4.0 38.1 1.0
NE2 B:HIS515 4.1 39.3 1.0
CG B:HIS519 4.2 33.1 1.0
CG B:HIS553 4.3 35.8 1.0
ND1 B:HIS519 4.3 34.9 1.0
CB B:ASP664 4.3 26.6 1.0
ND1 B:HIS553 4.4 38.1 1.0
CB B:ASP554 4.4 31.4 1.0
O B:HOH908 4.6 38.4 1.0
O B:HOH911 4.7 37.2 1.0
O B:HOH952 4.7 38.3 1.0
CA B:ASP664 4.8 26.4 1.0
CG2 B:VAL523 4.8 27.9 1.0
O B:ASP664 4.8 28.9 1.0
O B:HOH906 5.0 29.4 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: Sun Oct 27 13:41:25 2024

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