Zinc in PDB 5c1w: PDE10 Complexed with 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine

All present enzymatic activity of PDE10 Complexed with 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine:
3.1.4.17; 3.1.4.35;

The structure of PDE10 Complexed with 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine, PDB code: 5c1w was solved by Y.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.06 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.430, 81.850, 153.770, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 22.9

The structure of PDE10 Complexed with 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the PDE10 Complexed with 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine (pdb code 5c1w). 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 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine, PDB code: 5c1w:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the PDE10 Complexed with 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine


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 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:27.0 occ:1.00 O A:HOH923 2.0 19.3 1.0 OD2 A:ASP554 2.1 18.3 1.0 OD1 A:ASP664 2.1 17.3 1.0 NE2 A:HIS553 2.1 17.9 1.0 NE2 A:HIS519 2.2 19.2 1.0 O A:HOH979 2.3 20.2 1.0 CD2 A:HIS553 3.0 19.3 1.0 CG A:ASP664 3.0 25.6 1.0 CG A:ASP554 3.1 18.9 1.0 CD2 A:HIS519 3.1 19.5 1.0 CE1 A:HIS553 3.2 19.4 1.0 CE1 A:HIS519 3.3 18.2 1.0 OD2 A:ASP664 3.3 29.9 1.0 OD1 A:ASP554 3.6 18.4 1.0 MG A:MG802 3.7 20.3 1.0 O A:HOH1050 4.0 20.5 1.0 CD2 A:HIS515 4.0 25.1 1.0 O A:HOH950 4.2 28.8 1.0 CG A:HIS553 4.2 19.7 1.0 CB A:ASP554 4.3 16.6 1.0 ND1 A:HIS553 4.3 20.6 1.0 CG A:HIS519 4.3 17.7 1.0 CB A:ASP664 4.4 17.9 1.0 ND1 A:HIS519 4.4 18.3 1.0 NE2 A:HIS515 4.4 25.5 1.0 O A:HOH1084 4.7 43.0 1.0 O A:HOH911 4.7 18.9 1.0 CG2 A:VAL523 4.8 17.9 1.0 CA A:ASP664 4.8 16.3 1.0 O A:ASP664 4.9 18.8 1.0

Zinc binding site 2 out of 2 in the PDE10 Complexed with 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine


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 4,6-Dichloro-2-Cyclopropyl-5-Methyl-Pyrimidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:31.9 occ:1.00 O B:HOH911 2.0 21.5 1.0 O B:HOH930 2.1 26.6 1.0 NE2 B:HIS553 2.1 20.3 1.0 OD1 B:ASP664 2.2 20.2 1.0 OD2 B:ASP554 2.2 25.0 1.0 NE2 B:HIS519 2.2 26.5 1.0 CD2 B:HIS553 3.0 20.5 1.0 CG B:ASP664 3.1 26.7 1.0 CD2 B:HIS519 3.2 27.1 1.0 CG B:ASP554 3.2 26.8 1.0 CE1 B:HIS553 3.2 20.1 1.0 CE1 B:HIS519 3.3 26.7 1.0 OD2 B:ASP664 3.3 30.4 1.0 OD1 B:ASP554 3.7 22.2 1.0 MG B:MG802 3.7 21.8 1.0 O B:HOH913 3.8 50.5 1.0 O B:HOH1059 3.9 27.4 1.0 CG B:HIS553 4.2 19.6 1.0 ND1 B:HIS553 4.3 20.6 1.0 CB B:ASP554 4.3 22.1 1.0 CG B:HIS519 4.3 24.8 1.0 ND1 B:HIS519 4.4 26.6 1.0 CB B:ASP664 4.4 18.4 1.0 CD2 B:HIS515 4.6 37.6 1.0 O B:HOH914 4.6 22.6 1.0 CG2 B:VAL523 4.8 19.3 1.0 CA B:ASP664 4.9 17.1 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