Fluorine in PDB 6fr2: Soluble Epoxide Hydrolase in Complex with LK864

All present enzymatic activity of Soluble Epoxide Hydrolase in Complex with LK864:
3.1.3.76; 3.3.2.10;

The structure of Soluble Epoxide Hydrolase in Complex with LK864, PDB code: 6fr2 was solved by J.S.Kramer, D.Pogoryelov, M.Krasavin, E.Proschak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.09 / 2.26
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	80.091, 92.180, 106.998, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 21

The structure of Soluble Epoxide Hydrolase in Complex with LK864 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Soluble Epoxide Hydrolase in Complex with LK864 (pdb code 6fr2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Soluble Epoxide Hydrolase in Complex with LK864, PDB code: 6fr2:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Soluble Epoxide Hydrolase in Complex with LK864


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Soluble Epoxide Hydrolase in Complex with LK864 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:82.7 occ:0.58 F29 A:E3N601 0.0 82.7 0.6 C28 A:E3N601 1.3 83.3 1.0 F31 A:E3N601 2.1 80.4 0.6 F30 A:E3N601 2.1 85.2 0.5 O27 A:E3N601 2.2 82.5 1.0 C26 A:E3N601 2.8 78.9 1.0 O A:HOH805 3.0 63.7 1.0 C25 A:E3N601 3.2 75.3 1.0 CG A:MET419 3.2 83.9 1.0 CG2 A:VAL498 3.6 40.7 1.0 C32 A:E3N601 3.9 80.3 1.0 SD A:MET419 4.0 89.9 1.0 C24 A:E3N601 4.4 67.9 1.0 CB A:MET419 4.6 81.4 1.0 CE A:MET419 4.6 89.3 1.0 O A:HOH717 4.6 0.9 1.0 CB A:VAL498 4.8 49.1 1.0 C33 A:E3N601 4.9 74.6 1.0

Fluorine binding site 2 out of 3 in the Soluble Epoxide Hydrolase in Complex with LK864


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Soluble Epoxide Hydrolase in Complex with LK864 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:85.2 occ:0.54 F30 A:E3N601 0.0 85.2 0.5 C28 A:E3N601 1.3 83.3 1.0 F31 A:E3N601 2.1 80.4 0.6 F29 A:E3N601 2.1 82.7 0.6 O27 A:E3N601 2.2 82.5 1.0 O A:HOH713 3.2 46.7 1.0 O A:HOH805 3.4 63.7 1.0 OG A:SER415 3.5 76.7 1.0 C26 A:E3N601 3.5 78.9 1.0 O A:HOH771 3.5 48.2 1.0 O A:HOH717 3.8 0.9 1.0 C25 A:E3N601 4.2 75.3 1.0 C32 A:E3N601 4.5 80.3 1.0 CB A:SER415 4.6 71.3 1.0

Fluorine binding site 3 out of 3 in the Soluble Epoxide Hydrolase in Complex with LK864


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Soluble Epoxide Hydrolase in Complex with LK864 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:80.4 occ:0.58 F31 A:E3N601 0.0 80.4 0.6 C28 A:E3N601 1.3 83.3 1.0 F30 A:E3N601 2.1 85.2 0.5 F29 A:E3N601 2.1 82.7 0.6 O27 A:E3N601 2.3 82.5 1.0 C25 A:E3N601 3.0 75.3 1.0 C26 A:E3N601 3.0 78.9 1.0 O A:HOH717 3.1 0.9 1.0 O A:HOH805 3.4 63.7 1.0 O A:HOH771 3.5 48.2 1.0 CB A:HIS524 3.7 37.0 1.0 CG2 A:VAL498 4.0 40.7 1.0 OD1 A:ASP496 4.2 45.9 1.0 C24 A:E3N601 4.3 67.9 1.0 C32 A:E3N601 4.3 80.3 1.0 CG A:HIS524 4.4 39.9 1.0 O A:HOH713 4.5 46.7 1.0 N A:PHE497 4.6 38.9 1.0 N A:VAL498 4.6 46.4 1.0 CB A:VAL498 4.7 49.1 1.0 CA A:HIS524 4.9 36.8 1.0 N A:HIS524 4.9 45.0 1.0 ND1 A:HIS524 5.0 39.4 1.0

A.Lukin, J.Kramer, M.Hartmann, L.Weizel, V.Hernandez-Olmos, K.Falahati, I.Burghardt, N.Kalinchenkova, D.Bagnyukova, N.Zhurilo, J.Rautio, M.Forsberg, J.Ihalainen, S.Auriola, J.Leppanen, I.Konstantinov, D.Pogoryelov, E.Proschak, D.Dar'in, M.Krasavin. Discovery of Polar Spirocyclic Orally Bioavailable Urea Inhibitors of Soluble Epoxide Hydrolase. Bioorg. Chem. V. 80 655 2018.
ISSN: ISSN 1090-2120
PubMed: 30059891
DOI: 10.1016/J.BIOORG.2018.07.014