Zinc in PDB 5xui: Crystal Structure of PDE10A in Complex with 2-Methyl-5-[2-([1,2, 4]Triazolo[1,5-A]Pyrimidin-2-Yl)Et Hyl]Pyrazolo[1,5-A]Pyrimidin-7-Ol

Enzymatic activity of Crystal Structure of PDE10A in Complex with 2-Methyl-5-[2-([1,2, 4]Triazolo[1,5-A]Pyrimidin-2-Yl)Et Hyl]Pyrazolo[1,5-A]Pyrimidin-7-Ol

All present enzymatic activity of Crystal Structure of PDE10A in Complex with 2-Methyl-5-[2-([1,2, 4]Triazolo[1,5-A]Pyrimidin-2-Yl)Et Hyl]Pyrazolo[1,5-A]Pyrimidin-7-Ol:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of PDE10A in Complex with 2-Methyl-5-[2-([1,2, 4]Triazolo[1,5-A]Pyrimidin-2-Yl)Et Hyl]Pyrazolo[1,5-A]Pyrimidin-7-Ol, PDB code: 5xui was solved by Y.Amano, K.Honbou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.46 / 2.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.345, 81.443, 158.745, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 27.2

Other elements in 5xui:

The structure of Crystal Structure of PDE10A in Complex with 2-Methyl-5-[2-([1,2, 4]Triazolo[1,5-A]Pyrimidin-2-Yl)Et Hyl]Pyrazolo[1,5-A]Pyrimidin-7-Ol also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of PDE10A in Complex with 2-Methyl-5-[2-([1,2, 4]Triazolo[1,5-A]Pyrimidin-2-Yl)Et Hyl]Pyrazolo[1,5-A]Pyrimidin-7-Ol (pdb code 5xui). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of PDE10A in Complex with 2-Methyl-5-[2-([1,2, 4]Triazolo[1,5-A]Pyrimidin-2-Yl)Et Hyl]Pyrazolo[1,5-A]Pyrimidin-7-Ol, PDB code: 5xui:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5xui

Go back to Zinc Binding Sites List in 5xui
Zinc binding site 1 out of 2 in the Crystal Structure of PDE10A in Complex with 2-Methyl-5-[2-([1,2, 4]Triazolo[1,5-A]Pyrimidin-2-Yl)Et Hyl]Pyrazolo[1,5-A]Pyrimidin-7-Ol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of PDE10A in Complex with 2-Methyl-5-[2-([1,2, 4]Triazolo[1,5-A]Pyrimidin-2-Yl)Et Hyl]Pyrazolo[1,5-A]Pyrimidin-7-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:53.0
occ:1.00
 NE2 A:HIS563 1.7 54.2 1.0
OD2 A:ASP564 1.8 53.4 1.0
OD1 A:ASP674 2.1 58.5 1.0
NE2 A:HIS529 2.1 38.6 1.0
CE1 A:HIS563 2.2 56.2 1.0
O A:HOH901 2.4 41.9 1.0
OD2 A:ASP674 2.5 63.2 1.0
O A:HOH904 2.6 34.2 1.0
CG A:ASP674 2.7 53.4 1.0
CG A:ASP564 2.8 46.8 1.0
CE1 A:HIS529 3.0 42.1 1.0
CD2 A:HIS563 3.0 52.5 1.0
O A:HOH909 3.2 20.4 1.0
CD2 A:HIS529 3.3 43.0 1.0
OD1 A:ASP564 3.4 49.4 1.0
O A:HOH912 3.4 24.4 1.0
ND1 A:HIS563 3.5 47.4 1.0
O A:HOH902 3.8 19.0 1.0
CG A:HIS563 3.9 45.3 1.0
CB A:ASP564 4.0 44.3 1.0
MG A:MG802 4.1 53.6 1.0
ND1 A:HIS529 4.1 41.4 1.0
CD2 A:HIS525 4.2 57.2 1.0
CB A:ASP674 4.2 46.2 1.0
CG A:HIS529 4.3 44.0 1.0
O A:HOH905 4.3 37.4 1.0
NE2 A:HIS525 4.6 57.6 1.0
CA A:ASP674 4.8 44.9 1.0
O A:ASP674 4.9 42.4 1.0

Zinc binding site 2 out of 2 in 5xui

Go back to Zinc Binding Sites List in 5xui
Zinc binding site 2 out of 2 in the Crystal Structure of PDE10A in Complex with 2-Methyl-5-[2-([1,2, 4]Triazolo[1,5-A]Pyrimidin-2-Yl)Et Hyl]Pyrazolo[1,5-A]Pyrimidin-7-Ol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of PDE10A in Complex with 2-Methyl-5-[2-([1,2, 4]Triazolo[1,5-A]Pyrimidin-2-Yl)Et Hyl]Pyrazolo[1,5-A]Pyrimidin-7-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:52.8
occ:1.00
 NE2 B:HIS563 1.5 51.2 1.0
CE1 B:HIS563 1.7 49.2 1.0
OD2 B:ASP564 1.9 48.2 1.0
NE2 B:HIS529 2.1 34.7 1.0
OD1 B:ASP674 2.2 39.8 1.0
O B:HOH901 2.5 43.1 1.0
O B:HOH911 2.7 65.0 1.0
CG B:ASP564 2.9 43.4 1.0
CD2 B:HIS563 2.9 51.7 1.0
CG B:ASP674 2.9 37.5 1.0
O B:HOH909 3.0 18.4 1.0
ND1 B:HIS563 3.0 47.3 1.0
OD2 B:ASP674 3.0 39.8 1.0
CE1 B:HIS529 3.1 35.5 1.0
CD2 B:HIS529 3.1 37.1 1.0
OD1 B:ASP564 3.3 47.8 1.0
CG B:HIS563 3.5 45.3 1.0
MG B:MG802 3.6 40.0 1.0
CD2 B:HIS525 4.0 48.8 1.0
O B:HOH908 4.0 38.4 1.0
CB B:ASP564 4.1 41.4 1.0
ND1 B:HIS529 4.2 35.1 1.0
CG B:HIS529 4.3 34.9 1.0
CB B:ASP674 4.3 35.5 1.0
O B:HOH903 4.4 48.8 1.0
NE2 B:HIS525 4.4 46.9 1.0
O B:ASP674 4.7 41.5 1.0
CA B:ASP674 4.9 36.7 1.0
O B:HOH905 4.9 30.9 1.0
O B:HOH902 4.9 35.1 1.0
CG2 B:VAL533 4.9 34.8 1.0

Reference:

A.Chino, R.Seo, Y.Amano, I.Namatame, W.Hamaguchi, K.Honbou, T.Mihara, M.Yamazaki, M.Tomishima, N.Masuda. Fragment-Based Discovery of Pyrimido[1,2-B]Indazole PDE10A Inhibitors. Chem. Pharm. Bull. V. 66 286 2018.
ISSN: ISSN 1347-5223
PubMed: 29491261
DOI: 10.1248/CPB.C17-00836
Page generated: Wed Dec 16 11:21:15 2020

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