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Magnesium 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:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 5xui

Go back to Magnesium Binding Sites List in 5xui
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:53.6
occ:1.00
 O A:HOH905 1.8 37.4 1.0
OD1 A:ASP564 2.0 49.4 1.0
O A:HOH901 2.0 41.9 1.0
O A:HOH908 2.4 38.3 1.0
O A:HOH909 2.9 20.4 1.0
CG A:ASP564 3.1 46.8 1.0
CD2 A:HIS595 3.3 50.5 1.0
OG1 A:THR633 3.4 49.1 1.0
OE2 A:GLU592 3.4 66.3 1.0
NE2 A:HIS595 3.4 50.2 1.0
CD2 A:HIS563 3.5 52.5 1.0
O A:HIS563 3.5 41.9 1.0
OD2 A:ASP564 3.7 53.4 1.0
NE2 A:HIS563 3.8 54.2 1.0
ZN A:ZN801 4.1 53.0 1.0
CB A:THR633 4.1 48.0 1.0
CA A:ASP564 4.2 45.5 1.0
CB A:ASP564 4.2 44.3 1.0
CD A:GLU592 4.3 64.5 1.0
CG A:GLU592 4.3 62.8 1.0
C A:HIS563 4.3 46.5 1.0
O A:THR633 4.3 49.1 1.0
OD2 A:ASP674 4.4 63.2 1.0
CG A:HIS595 4.5 50.0 1.0
O A:HOH912 4.5 24.4 1.0
O A:HOH907 4.6 38.0 1.0
CE1 A:HIS595 4.6 50.8 1.0
CG A:HIS563 4.6 45.3 1.0
N A:ASP564 4.7 45.8 1.0
C A:THR633 4.8 48.2 1.0
O A:HOH902 4.9 19.0 1.0
CE1 A:HIS563 5.0 56.2 1.0

Magnesium binding site 2 out of 2 in 5xui

Go back to Magnesium Binding Sites List in 5xui
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:40.0
occ:1.00
 O B:HOH904 1.7 38.5 1.0
OD1 B:ASP564 1.9 47.8 1.0
O B:HOH901 1.9 43.1 1.0
O B:HOH905 2.1 30.9 1.0
O B:HOH909 2.2 18.4 1.0
O B:HOH902 2.6 35.1 1.0
CG B:ASP564 2.9 43.4 1.0
O B:HOH906 3.0 28.7 1.0
OD2 B:ASP564 3.3 48.2 1.0
NE2 B:HIS563 3.4 51.2 1.0
ZN B:ZN801 3.6 52.8 1.0
O B:HOH908 3.7 38.4 1.0
CD2 B:HIS563 3.8 51.7 1.0
NE2 B:HIS595 4.0 47.7 1.0
OE2 B:GLU592 4.1 53.1 1.0
CB B:ASP564 4.2 41.4 1.0
OG1 B:THR633 4.2 38.8 1.0
CD2 B:HIS567 4.3 40.6 1.0
CD2 B:HIS595 4.4 48.4 1.0
OD2 B:ASP674 4.4 39.8 1.0
O B:THR633 4.5 45.7 1.0
NE2 B:HIS567 4.5 38.0 1.0
CD2 B:HIS525 4.5 48.8 1.0
CE1 B:HIS563 4.6 49.2 1.0
NE2 B:HIS525 4.6 46.9 1.0
CA B:ASP564 4.6 46.3 1.0
O B:HOH903 4.6 48.8 1.0
O B:HIS563 4.7 44.9 1.0
O B:HOH911 4.8 65.0 1.0
CD B:GLU592 4.9 54.5 1.0
CB B:THR633 4.9 37.9 1.0
CG B:HIS563 5.0 45.3 1.0
CG B:GLU592 5.0 55.2 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: Mon Sep 30 09:44:15 2024

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