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Chlorine 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
Zinc (Zn) 2 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 2 in 5c2a

Go back to Chlorine Binding Sites List in 5c2a
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl803

b:41.7
occ:1.00
 CL A:4Y2803 0.0 41.7 1.0
C A:4Y2803 1.7 35.5 1.0
N A:4Y2803 2.6 32.2 1.0
C4 A:4Y2803 2.7 31.1 1.0
C5 A:4Y2803 3.0 30.2 1.0
CG1 A:VAL668 3.4 31.0 1.0
OE1 A:GLN716 3.5 38.5 1.0
O A:HOH955 3.6 31.9 1.0
O A:HOH906 3.6 29.1 1.0
C1 A:4Y2803 3.8 30.9 1.0
CD1 A:ILE682 3.9 28.7 1.0
C3 A:4Y2803 4.0 30.9 1.0
CE2 A:PHE719 4.0 38.2 1.0
NE2 A:GLN716 4.0 37.3 1.0
CD A:GLN716 4.2 47.6 1.0
CD2 A:PHE719 4.2 35.9 1.0
OG A:SER667 4.4 38.8 1.0
N2 A:4Y2803 4.4 32.9 1.0
CZ A:PHE719 4.8 36.0 1.0
CE1 A:TYR720 4.8 31.2 1.0
CB A:VAL668 4.9 31.5 1.0
C6 A:4Y2803 4.9 31.6 1.0

Chlorine binding site 2 out of 2 in 5c2a

Go back to Chlorine Binding Sites List in 5c2a
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl803

b:43.2
occ:1.00
 CL B:4Y2803 0.0 43.2 1.0
C B:4Y2803 1.7 36.6 1.0
N B:4Y2803 2.5 35.3 1.0
C4 B:4Y2803 2.7 34.8 1.0
C5 B:4Y2803 3.1 34.8 1.0
OE1 B:GLN716 3.4 36.6 1.0
CG1 B:VAL668 3.5 31.7 1.0
O B:HOH904 3.6 32.1 1.0
C1 B:4Y2803 3.8 34.6 1.0
O B:HOH947 3.8 39.6 1.0
CD1 B:ILE682 3.8 39.9 1.0
NE2 B:GLN716 3.9 36.1 1.0
C3 B:4Y2803 4.0 33.1 1.0
CE2 B:PHE719 4.0 34.6 1.0
CD B:GLN716 4.1 42.6 1.0
CD2 B:PHE719 4.1 33.8 1.0
N2 B:4Y2803 4.4 33.2 1.0
OG B:SER667 4.5 52.1 1.0
CE1 B:TYR720 4.8 35.3 1.0
CZ B:PHE719 4.9 32.2 1.0
C6 B:4Y2803 4.9 37.3 1.0
CB B:VAL668 5.0 32.6 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: Sat Jul 12 00:38:44 2025

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