Fluorine in PDB 3wk8: Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor

All present enzymatic activity of Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor:
3.1.3.76; 3.3.2.10;

The structure of Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor, PDB code: 3wk8 was solved by Y.Amano, T.Yamaguchi, E.Tanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.23 / 2.20
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.473, 92.473, 243.935, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 25.4

The structure of Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor (pdb code 3wk8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor, PDB code: 3wk8:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor


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 Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:23.0 occ:1.00 F12 A:S0E603 0.0 23.0 1.0 C4 A:S0E603 1.3 23.2 1.0 F13 A:S0E603 2.2 24.2 1.0 F14 A:S0E603 2.2 25.1 1.0 C7 A:S0E603 2.4 24.1 1.0 C10 A:S0E603 2.8 21.6 1.0 CD2 A:LEU428 3.4 31.2 1.0 C8 A:S0E603 3.5 22.0 1.0 CZ A:PHE387 3.6 24.6 1.0 CD2 A:LEU408 3.7 18.1 1.0 CE1 A:PHE267 4.1 13.7 1.0 C9 A:S0E603 4.2 21.8 1.0 CE2 A:PHE387 4.2 23.0 1.0 CD1 A:TYR383 4.3 22.6 1.0 CG A:LEU428 4.5 28.0 1.0 CE1 A:TYR383 4.5 20.7 1.0 CD1 A:LEU428 4.6 24.9 1.0 C5 A:S0E603 4.6 22.8 1.0 CD1 A:PHE267 4.6 13.5 1.0 CE1 A:PHE387 4.7 20.9 1.0 C6 A:S0E603 4.9 21.8 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor


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 Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:24.2 occ:1.00 F13 A:S0E603 0.0 24.2 1.0 C4 A:S0E603 1.4 23.2 1.0 F14 A:S0E603 2.1 25.1 1.0 F12 A:S0E603 2.2 23.0 1.0 C7 A:S0E603 2.3 24.1 1.0 C10 A:S0E603 3.0 21.6 1.0 C8 A:S0E603 3.3 22.0 1.0 CD2 A:LEU408 3.5 18.1 1.0 CE1 A:PHE267 3.5 13.7 1.0 CD1 A:PHE267 3.5 13.5 1.0 CD A:PRO268 3.7 12.0 1.0 O A:PHE267 3.9 14.2 1.0 CH2 A:TRP525 4.0 16.0 1.0 CG A:PRO268 4.2 11.6 1.0 C9 A:S0E603 4.2 21.8 1.0 CD1 A:LEU408 4.4 15.8 1.0 C5 A:S0E603 4.4 22.8 1.0 CG A:LEU408 4.5 17.0 1.0 C A:PHE267 4.5 12.8 1.0 N A:PRO268 4.5 12.3 1.0 CZ2 A:TRP525 4.5 14.9 1.0 C6 A:S0E603 4.8 21.8 1.0 CZ A:PHE267 4.8 13.8 1.0 CG A:PHE267 4.8 12.7 1.0 CZ A:PHE387 4.9 24.6 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor


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 Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:25.1 occ:1.00 F14 A:S0E603 0.0 25.1 1.0 C4 A:S0E603 1.4 23.2 1.0 F13 A:S0E603 2.1 24.2 1.0 F12 A:S0E603 2.2 23.0 1.0 C7 A:S0E603 2.4 24.1 1.0 C8 A:S0E603 2.7 22.0 1.0 CD1 A:PHE267 3.3 13.5 1.0 CE1 A:TYR383 3.4 20.7 1.0 CE1 A:PHE267 3.5 13.7 1.0 OH A:TYR466 3.6 22.1 1.0 C10 A:S0E603 3.6 21.6 1.0 CE2 A:PHE387 3.7 23.0 1.0 O A:HOH781 3.8 36.2 1.0 CD1 A:TYR383 3.9 22.6 1.0 CZ A:PHE387 3.9 24.6 1.0 C5 A:S0E603 4.1 22.8 1.0 CZ A:TYR383 4.4 24.2 1.0 O A:PHE267 4.5 14.2 1.0 CZ A:TYR466 4.6 19.6 1.0 CG A:PHE267 4.6 12.7 1.0 OH A:TYR383 4.7 25.0 1.0 C9 A:S0E603 4.8 21.8 1.0 CZ A:PHE267 4.8 13.8 1.0 C6 A:S0E603 4.9 21.8 1.0 CD2 A:PHE387 4.9 23.3 1.0

Y.Amano, T.Yamaguchi, E.Tanabe. Structural Insights Into Binding of Inhibitors to Soluble Epoxide Hydrolase Gained By Fragment Screening and X-Ray Crystallography Bioorg.Med.Chem. 2014.
ISSN: ESSN 1464-3391
PubMed: 24656800
DOI: 10.1016/J.BMC.2014.03.001