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Fluorine 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:

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 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 Fluorine atom.
In total 2 binding sites of Fluorine 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 Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 3wym

Go back to Fluorine Binding Sites List in 3wym
Fluorine 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 Fluorine with other atoms in the F 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:F1003

b:21.9
occ:1.00
 F28 A:3K91003 0.0 21.9 1.0
C18 A:3K91003 1.3 20.9 1.0
C19 A:3K91003 2.3 21.2 1.0
C17 A:3K91003 2.3 20.5 1.0
N16 A:3K91003 2.8 19.7 1.0
C29 A:3K91003 2.9 19.5 1.0
CD1 A:PHE719 3.5 18.1 1.0
C20 A:3K91003 3.6 21.5 1.0
C27 A:3K91003 3.6 20.6 1.0
CE1 A:PHE719 3.6 18.1 1.0
SD A:MET703 3.8 29.9 1.0
N15 A:3K91003 4.0 17.8 1.0
C30 A:3K91003 4.1 19.4 1.0
C26 A:3K91003 4.1 20.8 1.0
C32 A:3K91003 4.4 21.3 1.0
CE A:MET703 4.5 31.1 1.0
CD2 A:LEU625 4.6 20.8 1.0
O A:HOH1214 4.7 43.0 1.0
N21 A:3K91003 4.7 21.9 1.0
CG A:PHE719 4.8 18.1 1.0
O31 A:3K91003 4.8 20.5 1.0
C3 A:3K91003 4.9 18.3 1.0
CZ A:PHE719 4.9 18.0 1.0
N25 A:3K91003 5.0 23.1 1.0
C2 A:3K91003 5.0 18.9 1.0

Fluorine binding site 2 out of 2 in 3wym

Go back to Fluorine Binding Sites List in 3wym
Fluorine 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 Fluorine with other atoms in the F 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:F1003

b:25.9
occ:1.00
 F28 B:3K91003 0.0 25.9 1.0
C18 B:3K91003 1.3 25.2 1.0
C17 B:3K91003 2.3 24.0 1.0
C19 B:3K91003 2.4 25.1 1.0
N16 B:3K91003 2.8 22.8 1.0
C29 B:3K91003 2.9 22.3 1.0
CD1 B:PHE719 3.4 22.8 1.0
CE1 B:PHE719 3.5 22.5 1.0
C27 B:3K91003 3.6 23.9 1.0
C20 B:3K91003 3.6 25.9 1.0
CE B:MET703 3.7 30.5 1.0
N15 B:3K91003 3.9 22.3 1.0
C30 B:3K91003 4.0 21.7 1.0
C26 B:3K91003 4.1 25.0 1.0
SD B:MET703 4.2 28.9 1.0
C32 B:3K91003 4.4 21.9 1.0
CD2 B:LEU625 4.5 26.6 1.0
CG B:PHE719 4.7 23.2 1.0
CZ B:PHE719 4.7 22.5 1.0
N21 B:3K91003 4.8 27.0 1.0
O31 B:3K91003 4.8 22.4 1.0
C3 B:3K91003 4.8 21.0 1.0
C2 B:3K91003 5.0 21.4 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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