Atomistry » Fluorine » PDB 3wyl-460d » 3wym
Atomistry »
  Fluorine »
    PDB 3wyl-460d »
      3wym »

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: Sun Dec 13 11:57:55 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy