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Fluorine in PDB 5axp: Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-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-(2-Oxo-1,3-Oxazolidin-3-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-(2-Oxo-1,3-Oxazolidin-3-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-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One, PDB code: 5axp was solved by H.Oki, Y.Zama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.753, 81.849, 159.684, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 23.4

Other elements in 5axp:

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

Fluorine binding site 1 out of 2 in 5axp

Go back to Fluorine Binding Sites List in 5axp
Fluorine binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-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-(2-Oxo-1,3-Oxazolidin-3-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:37.6
occ:1.00
 F1 A:4LK1003 0.0 37.6 1.0
C2 A:4LK1003 1.3 34.9 1.0
C3 A:4LK1003 2.3 33.6 1.0
C13 A:4LK1003 2.3 31.0 1.0
N14 A:4LK1003 2.8 32.2 1.0
C28 A:4LK1003 2.9 29.1 1.0
CD1 A:PHE719 3.3 30.0 1.0
CE1 A:PHE719 3.4 25.5 1.0
C6 A:4LK1003 3.6 32.6 1.0
C4 A:4LK1003 3.6 31.2 1.0
O A:HOH1262 3.8 54.5 1.0
N15 A:4LK1003 3.9 28.5 1.0
C5 A:4LK1003 4.1 30.2 1.0
C29 A:4LK1003 4.1 30.7 1.0
O A:HOH1267 4.2 49.9 1.0
CD2 A:LEU625 4.4 43.3 1.0
C31 A:4LK1003 4.5 32.6 1.0
CG A:PHE719 4.6 31.3 1.0
O12 A:4LK1003 4.7 38.3 1.0
CZ A:PHE719 4.7 29.6 1.0
N7 A:4LK1003 4.8 32.6 1.0
C16 A:4LK1003 4.8 28.0 1.0
CG2 A:VAL723 4.8 28.9 1.0
O30 A:4LK1003 4.9 30.9 1.0
SD A:MET703 4.9 42.0 1.0
C32 A:4LK1003 5.0 28.7 1.0

Fluorine binding site 2 out of 2 in 5axp

Go back to Fluorine Binding Sites List in 5axp
Fluorine binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-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-(2-Oxo-1,3-Oxazolidin-3-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:36.6
occ:1.00
 F1 B:4LK1003 0.0 36.6 1.0
C2 B:4LK1003 1.3 36.5 1.0
C3 B:4LK1003 2.3 31.7 1.0
C13 B:4LK1003 2.4 33.7 1.0
N14 B:4LK1003 2.8 31.8 1.0
C28 B:4LK1003 3.1 32.1 1.0
CD1 B:PHE719 3.3 32.4 1.0
CE1 B:PHE719 3.3 30.2 1.0
C6 B:4LK1003 3.6 34.1 1.0
C4 B:4LK1003 3.6 36.5 1.0
N15 B:4LK1003 3.9 30.2 1.0
C5 B:4LK1003 4.1 35.0 1.0
C29 B:4LK1003 4.2 32.9 1.0
CG2 B:VAL723 4.5 30.1 1.0
CG B:PHE719 4.6 30.3 1.0
C31 B:4LK1003 4.6 30.3 1.0
O12 B:4LK1003 4.6 39.8 1.0
CD1 B:LEU625 4.7 37.1 1.0
CZ B:PHE719 4.7 33.1 1.0
C16 B:4LK1003 4.8 31.6 1.0
N7 B:4LK1003 4.8 37.9 1.0
C32 B:4LK1003 5.0 35.5 1.0

Reference:

M.Yoshikawa, H.Kamisaki, J.Kunitomo, H.Oki, H.Kokubo, A.Suzuki, T.Ikemoto, K.Nakashima, N.Kamiguchi, A.Harada, H.Kimura, T.Taniguchi. Design and Synthesis of A Novel 2-Oxindole Scaffold As A Highly Potent and Brain-Penetrant Phosphodiesterase 10A Inhibitor Bioorg.Med.Chem. V. 23 7138 2015.
ISSN: ESSN 1464-3391
PubMed: 26494583
DOI: 10.1016/J.BMC.2015.10.002
Page generated: Thu Aug 1 08:01:25 2024

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