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Magnesium in PDB 3wyl: Crystal Structure of the Catalytic Domain of PDE10A Complexed with 5- Methoxy-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 5- Methoxy-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 5- Methoxy-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 5- Methoxy-3-(1-Phenyl-1H-Pyrazol-5-Yl)-1-(3-(Trifluoromethyl)Phenyl) Pyridazin-4(1H)-One, PDB code: 3wyl 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) 37.71 / 2.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.881, 81.833, 162.156, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 26.1

Other elements in 3wyl:

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

Magnesium binding site 1 out of 2 in 3wyl

Go back to Magnesium Binding Sites List in 3wyl
Magnesium binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 5- Methoxy-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 5- Methoxy-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:Mg1002

b:30.3
occ:1.00
 OD1 A:ASP554 1.9 32.2 1.0
O A:HOH1102 1.9 33.6 1.0
O A:HOH1107 2.0 32.0 1.0
O A:HOH1106 2.0 26.7 1.0
O A:HOH1108 2.0 27.6 1.0
O A:HOH1103 2.1 22.2 1.0
CG A:ASP554 2.9 33.2 1.0
OD2 A:ASP554 3.2 35.9 1.0
OE2 A:GLU582 3.6 56.5 1.0
ZN A:ZN1001 3.7 46.9 1.0
NE2 A:HIS585 4.0 34.9 1.0
CD2 A:HIS553 4.2 33.5 1.0
CB A:ASP554 4.3 33.8 1.0
O A:HOH1116 4.3 38.7 1.0
CD2 A:HIS557 4.3 44.0 1.0
CD2 A:HIS585 4.3 34.7 1.0
O A:HIS553 4.3 40.9 1.0
NE2 A:HIS557 4.4 44.8 1.0
NE2 A:HIS515 4.4 46.5 1.0
NE2 A:HIS553 4.5 32.7 1.0
OD2 A:ASP664 4.5 50.7 1.0
CD2 A:HIS515 4.5 46.0 1.0
OG1 A:THR623 4.6 43.9 1.0
CA A:ASP554 4.7 34.4 1.0
CD A:GLU582 4.7 53.6 1.0
O A:THR623 4.8 47.9 1.0
CB A:THR623 4.8 45.3 1.0

Magnesium binding site 2 out of 2 in 3wyl

Go back to Magnesium Binding Sites List in 3wyl
Magnesium binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 5- Methoxy-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 5- Methoxy-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:Mg1002

b:43.9
occ:1.00
 O B:HOH1112 1.8 34.9 1.0
O B:HOH1103 2.0 39.6 1.0
O B:HOH1105 2.1 31.1 1.0
O B:HOH1111 2.2 45.8 1.0
O B:HOH1110 2.3 50.9 1.0
OD1 B:ASP554 2.4 30.3 1.0
CG B:ASP554 3.4 31.4 1.0
ZN B:ZN1001 3.7 42.1 1.0
OD2 B:ASP554 3.7 29.6 1.0
OD2 B:ASP664 3.9 46.7 1.0
O B:HIS553 4.1 41.9 1.0
O B:HOH1104 4.2 62.7 1.0
OG1 B:THR623 4.2 47.8 1.0
OE2 B:GLU582 4.3 65.0 1.0
CD2 B:HIS553 4.3 42.1 1.0
NE2 B:HIS585 4.5 43.0 1.0
CB B:THR623 4.5 47.5 1.0
O B:THR623 4.6 56.0 1.0
NE2 B:HIS557 4.7 47.7 1.0
CD2 B:HIS585 4.7 42.6 1.0
CB B:ASP554 4.7 32.8 1.0
CD2 B:HIS557 4.8 47.4 1.0
NE2 B:HIS553 4.8 43.5 1.0
NE2 B:HIS515 4.9 55.3 1.0
CG B:GLU582 4.9 59.7 1.0
CD2 B:HIS515 4.9 53.6 1.0
CG B:ASP664 4.9 43.4 1.0
C B:THR623 5.0 52.5 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 13:41:03 2024

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