Zinc in PDB 5c29: PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-N-Propyl- Pyrimidin-4-Amine

All present enzymatic activity of PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-N-Propyl- Pyrimidin-4-Amine:
3.1.4.17; 3.1.4.35;

The structure of PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-N-Propyl- Pyrimidin-4-Amine, PDB code: 5c29 was solved by Y.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.18 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.480, 81.190, 152.990, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 23.4

The structure of PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-N-Propyl- Pyrimidin-4-Amine also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-N-Propyl- Pyrimidin-4-Amine (pdb code 5c29). 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-5-Methyl-N-Propyl- Pyrimidin-4-Amine, PDB code: 5c29:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-N-Propyl- 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-5-Methyl-N-Propyl- Pyrimidin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:40.4 occ:1.00 OD1 A:ASP664 2.1 29.3 1.0 NE2 A:HIS553 2.1 31.5 1.0 OD2 A:ASP554 2.1 29.7 1.0 O A:HOH901 2.2 26.8 1.0 NE2 A:HIS519 2.2 29.6 1.0 O A:HOH968 2.5 25.8 1.0 CD2 A:HIS553 2.8 32.0 1.0 CG A:ASP664 3.0 33.4 1.0 CG A:ASP554 3.1 33.8 1.0 CE1 A:HIS519 3.2 29.6 1.0 CD2 A:HIS519 3.2 29.9 1.0 OD2 A:ASP664 3.3 40.9 1.0 CE1 A:HIS553 3.3 31.5 1.0 OD1 A:ASP554 3.5 32.8 1.0 MG A:MG802 3.6 27.6 1.0 O A:HOH973 4.0 28.3 1.0 CD2 A:HIS515 4.1 29.6 1.0 CG A:HIS553 4.1 31.4 1.0 O A:HOH958 4.3 32.7 1.0 CB A:ASP554 4.3 28.8 1.0 ND1 A:HIS553 4.3 32.4 1.0 NE2 A:HIS515 4.3 29.5 1.0 ND1 A:HIS519 4.3 31.2 1.0 CG A:HIS519 4.3 29.9 1.0 CB A:ASP664 4.4 28.0 1.0 O A:HOH1019 4.6 41.1 1.0 O A:HOH914 4.6 23.6 1.0 CA A:ASP664 4.8 26.6 1.0 O A:ASP664 4.8 33.0 1.0 CG2 A:VAL523 4.9 29.7 1.0 O A:HOH902 4.9 25.2 1.0

Zinc binding site 2 out of 2 in the PDE10 Complexed with 6-Chloro-2-Cyclopropyl-5-Methyl-N-Propyl- 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-5-Methyl-N-Propyl- Pyrimidin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:49.3 occ:1.00 O B:HOH907 2.1 38.0 1.0 OD2 B:ASP554 2.1 44.3 1.0 OD1 B:ASP664 2.2 27.2 1.0 NE2 B:HIS519 2.3 37.9 1.0 NE2 B:HIS553 2.3 34.2 1.0 O B:HOH974 2.4 31.7 1.0 CD2 B:HIS553 3.0 34.3 1.0 CG B:ASP664 3.0 30.9 1.0 CG B:ASP554 3.0 36.4 1.0 CE1 B:HIS519 3.2 37.5 1.0 OD2 B:ASP664 3.2 35.3 1.0 CD2 B:HIS519 3.3 38.5 1.0 OD1 B:ASP554 3.4 36.9 1.0 CE1 B:HIS553 3.4 34.1 1.0 MG B:MG802 3.7 43.9 1.0 O B:HOH989 4.0 34.2 1.0 CG B:HIS553 4.2 34.0 1.0 CB B:ASP554 4.3 34.3 1.0 ND1 B:HIS519 4.4 38.2 1.0 CG B:HIS519 4.4 37.2 1.0 CB B:ASP664 4.4 26.8 1.0 ND1 B:HIS553 4.5 34.5 1.0 O B:HOH905 4.5 40.6 1.0 O B:HOH931 4.8 42.6 1.0 CA B:ASP664 4.9 24.9 1.0 CD2 B:HIS515 4.9 60.9 1.0 O B:ASP664 4.9 29.3 1.0

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