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Magnesium in PDB 3wym: Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(1H-Pyrazol-1-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl-1H- Pyrazol-5-Yl)Pyridazin-4(1H)-One

Enzymatic activity of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(1H-Pyrazol-1-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl-1H- Pyrazol-5-Yl)Pyridazin-4(1H)-One

All present enzymatic activity of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(1H-Pyrazol-1-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl-1H- Pyrazol-5-Yl)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 1- (2-Fluoro-4-(1H-Pyrazol-1-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl-1H- Pyrazol-5-Yl)Pyridazin-4(1H)-One, PDB code: 3wym 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) 44.96 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.701, 81.707, 161.533, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21.5

Other elements in 3wym:

The structure of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(1H-Pyrazol-1-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl-1H- Pyrazol-5-Yl)Pyridazin-4(1H)-One also contains other interesting chemical elements:

Fluorine (F) 2 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 1- (2-Fluoro-4-(1H-Pyrazol-1-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl-1H- Pyrazol-5-Yl)Pyridazin-4(1H)-One (pdb code 3wym). 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 1- (2-Fluoro-4-(1H-Pyrazol-1-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl-1H- Pyrazol-5-Yl)Pyridazin-4(1H)-One, PDB code: 3wym:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3wym

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

b:17.8
occ:1.00
 O A:HOH1125 2.0 16.3 1.0
O A:HOH1108 2.0 15.5 1.0
O A:HOH1103 2.1 16.3 1.0
OD1 A:ASP554 2.1 17.8 1.0
O A:HOH1105 2.2 12.8 1.0
O A:HOH1112 2.2 16.4 1.0
CG A:ASP554 3.1 17.2 1.0
OD2 A:ASP554 3.4 17.0 1.0
ZN A:ZN1002 3.8 24.4 1.0
OE2 A:GLU582 4.0 21.0 1.0
NE2 A:HIS585 4.0 20.3 1.0
O A:HOH1115 4.0 18.2 1.0
OG1 A:THR623 4.1 17.9 1.0
O A:HOH1120 4.2 19.5 1.0
CD2 A:HIS585 4.2 19.4 1.0
O A:HIS553 4.3 17.5 1.0
CD2 A:HIS553 4.3 16.7 1.0
O A:THR623 4.4 18.1 1.0
CD2 A:HIS557 4.5 20.8 1.0
CB A:ASP554 4.5 17.2 1.0
OD2 A:ASP664 4.5 22.1 1.0
NE2 A:HIS515 4.6 18.4 1.0
CG A:GLU582 4.6 20.2 1.0
CD2 A:HIS515 4.7 18.2 1.0
NE2 A:HIS557 4.7 21.6 1.0
CD A:GLU582 4.7 20.8 1.0
CB A:THR623 4.7 18.2 1.0
NE2 A:HIS553 4.7 16.8 1.0
CA A:ASP554 4.8 17.4 1.0

Magnesium binding site 2 out of 2 in 3wym

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

b:22.1
occ:1.00
 O B:HOH1104 2.0 17.8 1.0
OD1 B:ASP554 2.1 20.7 1.0
O B:HOH1131 2.1 15.3 1.0
O B:HOH1106 2.2 23.2 1.0
O B:HOH1110 2.2 19.7 1.0
O B:HOH1116 2.2 16.9 1.0
CG B:ASP554 3.1 20.7 1.0
OD2 B:ASP554 3.4 20.4 1.0
ZN B:ZN1002 3.8 24.2 1.0
OG1 B:THR623 4.0 19.8 1.0
OE2 B:GLU582 4.0 24.2 1.0
NE2 B:HIS585 4.1 21.3 1.0
CD2 B:HIS553 4.1 18.4 1.0
O B:HOH1105 4.2 14.7 1.0
O B:HIS553 4.2 19.6 1.0
O B:HOH1140 4.3 29.7 1.0
CD2 B:HIS585 4.3 21.1 1.0
CB B:ASP554 4.5 20.3 1.0
OD2 B:ASP664 4.5 22.9 1.0
CD2 B:HIS557 4.5 22.6 1.0
O B:THR623 4.5 20.6 1.0
NE2 B:HIS553 4.6 18.4 1.0
CB B:THR623 4.6 19.2 1.0
CG B:GLU582 4.7 24.2 1.0
CD2 B:HIS515 4.7 21.2 1.0
NE2 B:HIS515 4.7 21.9 1.0
CA B:ASP554 4.8 20.9 1.0
NE2 B:HIS557 4.8 23.1 1.0
CD B:GLU582 4.8 24.5 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 13:41:08 2024

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