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Fluorine 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:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 6 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3wyl

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Fluorine binding site 1 out of 6 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 Fluorine with other atoms in the F 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:F1003

b:81.5
occ:1.00
 F10 A:3KB1003 0.0 81.5 1.0
C9 A:3KB1003 1.4 76.0 1.0
F12 A:3KB1003 2.2 81.7 1.0
F11 A:3KB1003 2.2 75.1 1.0
C8 A:3KB1003 2.4 66.0 1.0
C13 A:3KB1003 2.8 63.9 1.0
C7 A:3KB1003 3.6 57.7 1.0
C14 A:3KB1003 4.2 60.3 1.0
C6 A:3KB1003 4.8 54.2 1.0
C15 A:3KB1003 5.0 57.3 1.0

Fluorine binding site 2 out of 6 in 3wyl

Go back to Fluorine Binding Sites List in 3wyl
Fluorine binding site 2 out of 6 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 Fluorine with other atoms in the F 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
A:F1003

b:75.1
occ:1.00
 F11 A:3KB1003 0.0 75.1 1.0
C9 A:3KB1003 1.4 76.0 1.0
F12 A:3KB1003 2.2 81.7 1.0
F10 A:3KB1003 2.2 81.5 1.0
C8 A:3KB1003 2.4 66.0 1.0
C7 A:3KB1003 2.9 57.7 1.0
C13 A:3KB1003 3.5 63.9 1.0
C6 A:3KB1003 4.2 54.2 1.0
C14 A:3KB1003 4.6 60.3 1.0
CG2 A:VAL723 4.7 37.2 1.0
CZ A:PHE629 4.8 42.9 1.0
C15 A:3KB1003 4.9 57.3 1.0
CD1 A:PHE719 5.0 30.8 1.0
CE1 A:PHE719 5.0 30.3 1.0

Fluorine binding site 3 out of 6 in 3wyl

Go back to Fluorine Binding Sites List in 3wyl
Fluorine binding site 3 out of 6 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 Fluorine with other atoms in the F binding site number 3 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:F1003

b:81.7
occ:1.00
 F12 A:3KB1003 0.0 81.7 1.0
C9 A:3KB1003 1.4 76.0 1.0
F10 A:3KB1003 2.2 81.5 1.0
F11 A:3KB1003 2.2 75.1 1.0
C8 A:3KB1003 2.3 66.0 1.0
C7 A:3KB1003 2.9 57.7 1.0
C13 A:3KB1003 3.4 63.9 1.0
SD A:MET703 4.2 68.8 1.0
C6 A:3KB1003 4.2 54.2 1.0
C14 A:3KB1003 4.6 60.3 1.0
CE A:MET703 4.6 69.2 1.0
C15 A:3KB1003 4.9 57.3 1.0

Fluorine binding site 4 out of 6 in 3wyl

Go back to Fluorine Binding Sites List in 3wyl
Fluorine binding site 4 out of 6 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 Fluorine with other atoms in the F binding site number 4 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:F1003

b:79.4
occ:1.00
 F10 B:3KB1003 0.0 79.4 1.0
C9 B:3KB1003 1.4 77.5 1.0
F11 B:3KB1003 2.2 75.1 1.0
F12 B:3KB1003 2.2 80.2 1.0
C8 B:3KB1003 2.4 72.8 1.0
C13 B:3KB1003 3.0 70.0 1.0
C7 B:3KB1003 3.5 66.0 1.0
CB B:SER561 4.1 61.9 1.0
CE B:MET703 4.3 73.4 1.0
C14 B:3KB1003 4.3 67.8 1.0
C6 B:3KB1003 4.6 62.2 1.0
OG B:SER561 4.9 62.7 1.0
C15 B:3KB1003 5.0 65.6 1.0

Fluorine binding site 5 out of 6 in 3wyl

Go back to Fluorine Binding Sites List in 3wyl
Fluorine binding site 5 out of 6 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 Fluorine with other atoms in the F binding site number 5 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:F1003

b:75.1
occ:1.00
 F11 B:3KB1003 0.0 75.1 1.0
C9 B:3KB1003 1.4 77.5 1.0
F12 B:3KB1003 2.2 80.2 1.0
F10 B:3KB1003 2.2 79.4 1.0
C8 B:3KB1003 2.4 72.8 1.0
C7 B:3KB1003 2.8 66.0 1.0
C26 B:3KB1003 2.9 50.6 1.0
C27 B:3KB1003 3.4 51.2 1.0
C25 B:3KB1003 3.5 50.8 1.0
C13 B:3KB1003 3.7 70.0 1.0
C6 B:3KB1003 4.2 62.2 1.0
C28 B:3KB1003 4.4 52.4 1.0
CE1 B:PHE686 4.4 44.0 1.0
C24 B:3KB1003 4.5 50.4 1.0
CZ B:PHE686 4.7 43.9 1.0
CD1 B:LEU625 4.7 71.4 1.0
C14 B:3KB1003 4.8 67.8 1.0
C23 B:3KB1003 4.9 51.2 1.0
N5 B:3KB1003 5.0 56.6 1.0
C15 B:3KB1003 5.0 65.6 1.0

Fluorine binding site 6 out of 6 in 3wyl

Go back to Fluorine Binding Sites List in 3wyl
Fluorine binding site 6 out of 6 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 Fluorine with other atoms in the F binding site number 6 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:F1003

b:80.2
occ:1.00
 F12 B:3KB1003 0.0 80.2 1.0
C9 B:3KB1003 1.4 77.5 1.0
F11 B:3KB1003 2.2 75.1 1.0
F10 B:3KB1003 2.2 79.4 1.0
C8 B:3KB1003 2.4 72.8 1.0
C13 B:3KB1003 3.0 70.0 1.0
C7 B:3KB1003 3.5 66.0 1.0
CD1 B:LEU625 3.8 71.4 1.0
CB B:LEU625 4.1 66.1 1.0
C14 B:3KB1003 4.3 67.8 1.0
C26 B:3KB1003 4.3 50.6 1.0
C27 B:3KB1003 4.3 51.2 1.0
CG B:LEU625 4.4 68.1 1.0
C6 B:3KB1003 4.6 62.2 1.0
C15 B:3KB1003 4.9 65.6 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: Mon Jul 14 20:09:52 2025

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