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Magnesium in PDB 3wyk: Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One

Enzymatic activity of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One

All present enzymatic activity of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One, PDB code: 3wyk was solved by H.Oki, Y.Hayano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.49 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.696, 81.696, 161.192, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 25

Other elements in 3wyk:

The structure of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One (pdb code 3wyk). 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 the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One, PDB code: 3wyk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3wyk

Go back to Magnesium Binding Sites List in 3wyk
Magnesium binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(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 the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:31.2
occ:1.00
 O A:HOH1144 1.9 25.2 1.0
O A:HOH1149 2.0 32.4 1.0
O A:HOH1170 2.0 25.8 1.0
O A:HOH1169 2.1 24.8 1.0
O A:HOH1171 2.2 25.1 1.0
OD1 A:ASP554 2.3 30.0 1.0
CG A:ASP554 3.3 29.5 1.0
OD2 A:ASP554 3.5 29.1 1.0
OE2 A:GLU582 3.7 36.7 1.0
ZN A:ZN1002 3.9 35.3 1.0
NE2 A:HIS585 4.0 32.2 1.0
O A:HOH1168 4.0 32.5 1.0
CD2 A:HIS553 4.3 27.5 1.0
CD2 A:HIS585 4.3 32.1 1.0
OG1 A:THR623 4.4 30.0 1.0
O A:HIS553 4.4 31.2 1.0
CD2 A:HIS557 4.5 32.0 1.0
O A:THR623 4.5 30.7 1.0
O A:HOH1161 4.5 31.3 1.0
OD2 A:ASP664 4.6 35.1 1.0
CB A:ASP554 4.6 30.2 1.0
CD A:GLU582 4.6 37.3 1.0
NE2 A:HIS515 4.6 30.8 1.0
NE2 A:HIS553 4.6 27.1 1.0
CD2 A:HIS515 4.6 30.7 1.0
NE2 A:HIS557 4.6 32.4 1.0
CG A:GLU582 4.8 36.4 1.0
CB A:THR623 4.8 29.1 1.0
CA A:ASP554 4.9 30.8 1.0

Magnesium binding site 2 out of 2 in 3wyk

Go back to Magnesium Binding Sites List in 3wyk
Magnesium binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(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 the Catalytic Domain of PDE10A Complexed with 3- (1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl)Pyridazin- 4(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:27.8
occ:1.00
 O B:HOH1166 2.0 31.7 1.0
OD1 B:ASP554 2.1 32.2 1.0
O B:HOH1112 2.1 24.8 1.0
O B:HOH1163 2.1 25.4 1.0
O B:HOH1113 2.1 33.8 1.0
O B:HOH1164 2.3 29.9 1.0
CG B:ASP554 3.2 32.1 1.0
OD2 B:ASP554 3.6 31.6 1.0
OE2 B:GLU582 3.8 38.9 1.0
ZN B:ZN1002 3.9 34.7 1.0
O B:HIS553 4.0 33.5 1.0
NE2 B:HIS585 4.0 33.5 1.0
OG1 B:THR623 4.0 31.4 1.0
CD2 B:HIS585 4.2 33.8 1.0
CD2 B:HIS553 4.2 31.3 1.0
O B:HOH1146 4.3 32.5 1.0
O B:HOH1162 4.3 34.7 1.0
OD2 B:ASP664 4.4 34.5 1.0
CD2 B:HIS557 4.5 36.3 1.0
CG B:GLU582 4.5 37.3 1.0
CB B:ASP554 4.5 32.3 1.0
O B:THR623 4.5 33.6 1.0
CD B:GLU582 4.6 38.3 1.0
NE2 B:HIS557 4.7 36.8 1.0
NE2 B:HIS553 4.7 31.0 1.0
CA B:ASP554 4.7 33.5 1.0
CB B:THR623 4.7 31.5 1.0
NE2 B:HIS515 4.8 31.9 1.0
CD2 B:HIS515 4.8 31.6 1.0
C B:HIS553 4.9 32.7 1.0

Reference:

J.Kunitomo, M.Yoshikawa, M.Fushimi, A.Kawada, F.J.Quinn, H.Oki, H.Kokubo, M.Kondo, K.Nakashima, N.Kamiguchi, K.Suzuki, H.Kimura, T.Taniguchi. Discovery of 1‑[2-Fluoro-4-(1H‑Pyrazol-1-Yl)Phenyl]-5- Methoxy-3-(1-Pheny‑1H‑Pyrazol-5-Yl)Pyridazin- 4(1H)‑One (Tak-063), A Highly Potent, Selective, and Orally Active Phosphodiesterase 10A (PDE10A)Inhibitor J.Med.Chem. 2014.
ISSN: ISSN 0022-2623
DOI: 10.1021/JM5013648
Page generated: Thu Aug 15 13:40:49 2024

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