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Fluorine 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:

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

Fluorine binding site 1 out of 6 in 3wyk

Go back to Fluorine Binding Sites List in 3wyk
Fluorine binding site 1 out of 6 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 Fluorine with other atoms in the F 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:F1003

b:47.8
occ:1.00
 F23 A:3KG1003 0.0 47.8 1.0
C22 A:3KG1003 1.4 47.4 1.0
F24 A:3KG1003 2.2 49.6 1.0
F25 A:3KG1003 2.2 50.0 1.0
C21 A:3KG1003 2.4 44.3 1.0
C20 A:3KG1003 3.0 42.6 1.0
C26 A:3KG1003 3.4 41.8 1.0
C19 A:3KG1003 4.3 40.7 1.0
CZ A:PHE629 4.5 37.4 1.0
CD2 A:LEU625 4.6 38.9 1.0
C17 A:3KG1003 4.6 39.1 1.0
CE1 A:PHE629 4.9 37.5 1.0
C18 A:3KG1003 4.9 39.3 1.0
CG2 A:VAL723 5.0 33.0 1.0

Fluorine binding site 2 out of 6 in 3wyk

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Fluorine binding site 2 out of 6 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 Fluorine with other atoms in the F 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
A:F1003

b:49.6
occ:1.00
 F24 A:3KG1003 0.0 49.6 1.0
C22 A:3KG1003 1.4 47.4 1.0
F25 A:3KG1003 2.2 50.0 1.0
F23 A:3KG1003 2.2 47.8 1.0
C21 A:3KG1003 2.4 44.3 1.0
C26 A:3KG1003 2.7 41.8 1.0
C20 A:3KG1003 3.7 42.6 1.0
C17 A:3KG1003 4.1 39.1 1.0
SD A:MET703 4.5 56.7 1.0
CD1 A:PHE719 4.6 30.9 1.0
C19 A:3KG1003 4.8 40.7 1.0
N16 A:3KG1003 4.9 37.5 1.0
C18 A:3KG1003 4.9 39.3 1.0
C27 A:3KG1003 4.9 37.8 1.0

Fluorine binding site 3 out of 6 in 3wyk

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

b:50.0
occ:1.00
 F25 A:3KG1003 0.0 50.0 1.0
C22 A:3KG1003 1.4 47.4 1.0
F24 A:3KG1003 2.2 49.6 1.0
F23 A:3KG1003 2.2 47.8 1.0
C21 A:3KG1003 2.4 44.3 1.0
C20 A:3KG1003 3.0 42.6 1.0
C26 A:3KG1003 3.4 41.8 1.0
C19 A:3KG1003 4.2 40.7 1.0
CE A:MET703 4.3 57.0 1.0
SD A:MET703 4.4 56.7 1.0
C17 A:3KG1003 4.6 39.1 1.0
C18 A:3KG1003 4.9 39.3 1.0

Fluorine binding site 4 out of 6 in 3wyk

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

b:81.7
occ:1.00
 F23 B:3KG1003 0.0 81.7 1.0
C22 B:3KG1003 1.4 77.4 1.0
F24 B:3KG1003 2.2 79.8 1.0
F25 B:3KG1003 2.2 82.2 1.0
C21 B:3KG1003 2.4 69.6 1.0
C20 B:3KG1003 2.9 64.4 1.0
C26 B:3KG1003 3.6 63.2 1.0
CD2 B:LEU625 3.9 42.9 1.0
C19 B:3KG1003 4.3 58.9 1.0
CZ B:PHE629 4.3 42.6 1.0
CE1 B:PHE629 4.5 42.5 1.0
C17 B:3KG1003 4.7 55.9 1.0
CG B:LEU625 5.0 42.4 1.0
C18 B:3KG1003 5.0 56.7 1.0

Fluorine binding site 5 out of 6 in 3wyk

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

b:79.8
occ:1.00
 F24 B:3KG1003 0.0 79.8 1.0
C22 B:3KG1003 1.4 77.4 1.0
F25 B:3KG1003 2.2 82.2 1.0
F23 B:3KG1003 2.2 81.7 1.0
C21 B:3KG1003 2.4 69.6 1.0
C26 B:3KG1003 2.7 63.2 1.0
C20 B:3KG1003 3.7 64.4 1.0
CD1 B:PHE719 4.0 41.6 1.0
C17 B:3KG1003 4.1 55.9 1.0
CE1 B:PHE719 4.3 40.1 1.0
CG2 B:VAL723 4.5 40.8 1.0
C19 B:3KG1003 4.8 58.9 1.0
CD2 B:LEU625 4.8 42.9 1.0
N16 B:3KG1003 4.9 50.2 1.0
C18 B:3KG1003 4.9 56.7 1.0

Fluorine binding site 6 out of 6 in 3wyk

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

b:82.2
occ:1.00
 F25 B:3KG1003 0.0 82.2 1.0
C22 B:3KG1003 1.4 77.4 1.0
F24 B:3KG1003 2.2 79.8 1.0
F23 B:3KG1003 2.2 81.7 1.0
C21 B:3KG1003 2.3 69.6 1.0
C20 B:3KG1003 3.0 64.4 1.0
C26 B:3KG1003 3.2 63.2 1.0
CE B:MET703 3.9 52.4 1.0
SD B:MET703 4.2 52.9 1.0
C19 B:3KG1003 4.3 58.9 1.0
C17 B:3KG1003 4.4 55.9 1.0
C18 B:3KG1003 4.8 56.7 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: Mon Jul 14 20:07:20 2025

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