Atomistry » Zinc » PDB 5brv-5c3k » 5c2a
Atomistry »
  Zinc »
    PDB 5brv-5c3k »
      5c2a »

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

Last articles

Na in 8B4V
Na in 8B4F
Na in 8B3U
Na in 8B3V
Na in 8B01
Na in 8B3T
Na in 8B3L
Na in 8ATE
Na in 8AWI
Na in 8AX3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy