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Magnesium in PDB 4wn1: Crystal Structure of PDE10A in Complex with 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One

Enzymatic activity of Crystal Structure of PDE10A in Complex with 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One

All present enzymatic activity of Crystal Structure of PDE10A in Complex with 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of PDE10A in Complex with 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One, PDB code: 4wn1 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) 79.61 / 3.13
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.294, 81.727, 159.210, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 32

Other elements in 4wn1:

The structure of Crystal Structure of PDE10A in Complex with 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One 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 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One (pdb code 4wn1). 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 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One, PDB code: 4wn1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4wn1

Go back to Magnesium Binding Sites List in 4wn1
Magnesium binding site 1 out of 2 in the Crystal Structure of PDE10A in Complex with 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One


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 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:21.8
occ:1.00
 O A:HOH906 1.7 20.9 1.0
O A:HOH904 1.8 6.2 1.0
O A:HOH903 1.9 14.2 1.0
O A:HOH902 2.1 21.1 1.0
OD1 A:ASP564 2.6 26.7 1.0
O A:HOH905 2.7 23.9 1.0
ZN A:ZN801 3.2 26.1 1.0
CG A:ASP564 3.4 27.7 1.0
OD2 A:ASP564 3.5 27.3 1.0
O A:HOH901 3.5 4.6 1.0
OD2 A:ASP674 3.9 25.5 1.0
OG1 A:THR633 4.2 40.7 1.0
CD2 A:HIS563 4.2 37.2 1.0
O A:THR633 4.2 42.4 1.0
OE2 A:GLU592 4.3 37.6 1.0
CB A:THR633 4.4 39.9 1.0
NE2 A:HIS563 4.5 38.2 1.0
NE2 A:HIS525 4.6 36.0 1.0
CD2 A:HIS525 4.6 35.9 1.0
NE2 A:HIS595 4.6 42.2 1.0
OD1 A:ASP674 4.7 25.2 1.0
CG A:ASP674 4.7 25.9 1.0
O A:HIS563 4.8 31.4 1.0
CB A:ASP564 4.9 28.4 1.0
CD2 A:HIS567 4.9 44.6 1.0
CD2 A:HIS595 4.9 42.2 1.0
C A:THR633 5.0 39.2 1.0

Magnesium binding site 2 out of 2 in 4wn1

Go back to Magnesium Binding Sites List in 4wn1
Magnesium binding site 2 out of 2 in the Crystal Structure of PDE10A in Complex with 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One


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 1-Methyl-5-(1-Methyl-3- {[4-(Quinolin-2-Yl)Phenoxy]Methyl}-1H-Pyrazol-4-Yl)Pyridin-2(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:13.5
occ:1.00
 O B:HOH907 1.6 9.3 1.0
O B:HOH902 2.0 12.5 1.0
O B:HOH904 2.1 12.4 1.0
O B:HOH906 2.3 13.2 1.0
O B:HOH905 2.3 8.0 1.0
OD1 B:ASP564 2.5 12.5 1.0
CG B:ASP564 3.3 12.9 1.0
O B:HOH901 3.3 9.2 1.0
OD2 B:ASP564 3.3 12.4 1.0
ZN B:ZN801 3.4 22.0 1.0
O B:HOH908 3.7 31.7 1.0
CD2 B:HIS563 3.8 14.0 1.0
OD2 B:ASP674 3.9 12.4 1.0
OE2 B:GLU592 3.9 19.6 1.0
CB B:THR633 4.1 14.5 1.0
O B:HOH903 4.1 6.9 1.0
OG1 B:THR633 4.1 14.5 1.0
O B:THR633 4.1 15.8 1.0
NE2 B:HIS563 4.2 14.1 1.0
O B:HIS563 4.4 15.4 1.0
C B:THR633 4.6 15.4 1.0
NE2 B:HIS595 4.7 23.8 1.0
CB B:ASP564 4.7 13.7 1.0
CG B:ASP674 4.7 12.3 1.0
OD1 B:ASP674 4.7 12.1 1.0
CD2 B:HIS525 4.8 32.1 1.0
CD B:GLU592 4.9 20.6 1.0
CD2 B:HIS595 4.9 23.5 1.0
CG B:GLU592 4.9 22.1 1.0
CG2 B:THR633 5.0 14.1 1.0

Reference:

W.Hamaguchi, N.Masuda, S.Miyamoto, Y.Shiina, S.Kikuchi, T.Mihara, H.Moriguchi, H.Fushiki, Y.Murakami, Y.Amano, K.Honbou, K.Hattori. Synthesis, Sar Study, and Biological Evaluation of Novel Quinoline Derivatives As Phosphodiesterase 10A Inhibitors with Reduced CYP3A4 Inhibition. Bioorg.Med.Chem. V. 23 297 2015.
ISSN: ESSN 1464-3391
PubMed: 25515954
DOI: 10.1016/J.BMC.2014.11.039
Page generated: Tue Aug 20 13:53:34 2024

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