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Fluorine in PDB 5axq: Crystal Structure of the Catalytic Domain of PDE10A Complexed with Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold

Enzymatic activity of Crystal Structure of the Catalytic Domain of PDE10A Complexed with Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold

All present enzymatic activity of Crystal Structure of the Catalytic Domain of PDE10A Complexed with Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of PDE10A Complexed with Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold, PDB code: 5axq 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 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.685, 81.793, 159.849, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.1

Other elements in 5axq:

The structure of Crystal Structure of the Catalytic Domain of PDE10A Complexed with Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold 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 Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold (pdb code 5axq). 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 Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold, PDB code: 5axq:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5axq

Go back to Fluorine Binding Sites List in 5axq
Fluorine binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold


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 Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:31.7
occ:1.00
F8 A:4LP1003 0.0 31.7 1.0
C7 A:4LP1003 1.3 29.0 1.0
C9 A:4LP1003 2.3 32.1 1.0
C6 A:4LP1003 2.4 26.1 1.0
N5 A:4LP1003 2.8 25.7 1.0
C4 A:4LP1003 2.8 25.7 1.0
C10 A:4LP1003 3.0 36.6 1.0
C11 A:4LP1003 3.2 41.6 1.0
C12 A:4LP1003 3.2 40.5 1.0
CD1 A:PHE719 3.3 26.2 1.0
O A:HOH1286 3.5 49.2 1.0
CE1 A:PHE719 3.6 21.5 1.0
C20 A:4LP1003 3.6 33.9 1.0
C22 A:4LP1003 3.6 28.8 1.0
N23 A:4LP1003 4.0 23.1 1.0
C3 A:4LP1003 4.0 25.9 1.0
SD A:MET703 4.1 38.1 1.0
C21 A:4LP1003 4.1 31.2 1.0
C1 A:4LP1003 4.2 30.3 1.0
C13 A:4LP1003 4.4 39.3 1.0
CG A:PHE719 4.5 25.7 1.0
N14 A:4LP1003 4.6 35.3 1.0
O2 A:4LP1003 4.7 28.3 1.0
C24 A:4LP1003 4.9 23.6 1.0
CZ A:PHE719 4.9 24.0 1.0
CE A:MET703 4.9 39.3 1.0
C36 A:4LP1003 4.9 24.5 1.0
CD2 A:LEU625 4.9 33.4 1.0
CB A:PHE719 5.0 25.4 1.0

Fluorine binding site 2 out of 2 in 5axq

Go back to Fluorine Binding Sites List in 5axq
Fluorine binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold


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 Highly Potent and Brain-Penetrant PDE10A Inhibitor with 2-Oxindole Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:38.9
occ:1.00
F1 B:4LK1003 0.0 38.9 1.0
C2 B:4LK1003 1.3 38.2 1.0
C3 B:4LK1003 2.3 35.8 1.0
C13 B:4LK1003 2.4 32.9 1.0
N14 B:4LK1003 2.8 31.0 1.0
C28 B:4LK1003 3.0 31.0 1.0
CD1 B:PHE719 3.3 29.0 1.0
CE1 B:PHE719 3.4 29.3 1.0
C4 B:4LK1003 3.6 36.8 1.0
C6 B:4LK1003 3.6 34.9 1.0
N15 B:4LK1003 3.8 28.0 1.0
C5 B:4LK1003 4.1 34.8 1.0
C29 B:4LK1003 4.1 28.8 1.0
CD2 B:LEU625 4.2 39.0 1.0
CG2 B:VAL723 4.5 33.0 1.0
CG B:PHE719 4.6 29.5 1.0
C31 B:4LK1003 4.6 33.1 1.0
O12 B:4LK1003 4.6 38.4 1.0
CZ B:PHE719 4.7 27.6 1.0
C16 B:4LK1003 4.7 26.6 1.0
N7 B:4LK1003 4.8 36.5 1.0
C32 B:4LK1003 4.9 28.5 1.0
O30 B:4LK1003 5.0 35.4 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 08:01:26 2024

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