Fluorine in PDB 5akh: Ligand Complex Structure of Soluble Epoxide Hydrolase

All present enzymatic activity of Ligand Complex Structure of Soluble Epoxide Hydrolase:
3.1.3.76; 3.3.2.10;

The structure of Ligand Complex Structure of Soluble Epoxide Hydrolase, PDB code: 5akh was solved by L.Oster, S.Tapani, Y.Xue, H.Kack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.45 / 2.10
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.892, 92.892, 243.802, 90.00, 90.00, 120.00
R / Rfree (%)	18.21 / 23.32

The binding sites of Fluorine atom in the Ligand Complex Structure of Soluble Epoxide Hydrolase (pdb code 5akh). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Ligand Complex Structure of Soluble Epoxide Hydrolase, PDB code: 5akh:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Ligand Complex Structure of Soluble Epoxide Hydrolase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ligand Complex Structure of Soluble Epoxide Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:F1552 b:32.2 occ:1.00 F8 A:6NM1552 0.0 32.2 1.0 C7 A:6NM1552 1.4 29.7 1.0 F9 A:6NM1552 2.2 30.3 1.0 F10 A:6NM1552 2.2 28.4 1.0 C5 A:6NM1552 2.4 28.4 1.0 C6 A:6NM1552 2.9 26.7 1.0 CD2 A:LEU408 3.5 24.6 1.0 CZ A:PHE387 3.5 22.9 1.0 C4 A:6NM1552 3.6 29.4 1.0 CD2 A:LEU428 3.8 35.2 1.0 CG A:LEU428 4.1 34.9 1.0 CE2 A:PHE387 4.2 25.1 1.0 C1 A:6NM1552 4.2 25.8 1.0 CE1 A:PHE267 4.2 17.7 1.0 CD1 A:LEU428 4.4 34.5 1.0 CE1 A:PHE387 4.5 23.3 1.0 CD1 A:TYR383 4.7 30.5 1.0 CD1 A:PHE267 4.7 17.5 1.0 CG A:LEU408 4.8 22.1 1.0 C3 A:6NM1552 4.8 29.2 1.0 CD1 A:LEU408 4.8 21.0 1.0

Fluorine binding site 2 out of 3 in the Ligand Complex Structure of Soluble Epoxide Hydrolase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ligand Complex Structure of Soluble Epoxide Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:F1552 b:30.3 occ:1.00 F9 A:6NM1552 0.0 30.3 1.0 C7 A:6NM1552 1.4 29.7 1.0 F8 A:6NM1552 2.2 32.2 1.0 F10 A:6NM1552 2.2 28.4 1.0 C5 A:6NM1552 2.4 28.4 1.0 CD1 A:TYR383 3.1 30.5 1.0 C4 A:6NM1552 3.1 29.4 1.0 C6 A:6NM1552 3.3 26.7 1.0 CG A:TYR383 3.3 29.4 1.0 CB A:TYR383 3.5 26.6 1.0 CD1 A:LEU428 3.6 34.5 1.0 SD A:MET419 3.8 46.0 1.0 CZ A:PHE387 3.8 22.9 1.0 CE1 A:TYR383 3.8 31.4 1.0 CG A:LEU428 4.1 34.9 1.0 CD2 A:LEU428 4.1 35.2 1.0 CE A:MET419 4.2 42.3 1.0 CD2 A:TYR383 4.2 30.3 1.0 CE2 A:PHE387 4.3 25.1 1.0 C3 A:6NM1552 4.4 29.2 1.0 C1 A:6NM1552 4.5 25.8 1.0 CZ A:TYR383 4.6 39.4 1.0 CE1 A:PHE387 4.6 23.3 1.0 CE2 A:TYR383 4.8 31.4 1.0 CA A:TYR383 4.9 24.5 1.0 C2 A:6NM1552 4.9 26.2 1.0

Fluorine binding site 3 out of 3 in the Ligand Complex Structure of Soluble Epoxide Hydrolase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ligand Complex Structure of Soluble Epoxide Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:F1552 b:28.4 occ:1.00 F10 A:6NM1552 0.0 28.4 1.0 C7 A:6NM1552 1.4 29.7 1.0 F9 A:6NM1552 2.2 30.3 1.0 F8 A:6NM1552 2.2 32.2 1.0 C5 A:6NM1552 2.3 28.4 1.0 C4 A:6NM1552 2.7 29.4 1.0 CE A:MET419 3.3 42.3 1.0 CD2 A:LEU408 3.4 24.6 1.0 C6 A:6NM1552 3.6 26.7 1.0 SD A:MET419 3.7 46.0 1.0 CD1 A:LEU417 3.9 48.7 1.0 C17 A:6NM1552 4.0 31.3 1.0 C3 A:6NM1552 4.1 29.2 1.0 CD1 A:LEU428 4.1 34.5 1.0 CG A:LEU428 4.2 34.9 1.0 C18 A:6NM1552 4.2 33.6 1.0 C16 A:6NM1552 4.6 31.8 1.0 CD2 A:LEU428 4.6 35.2 1.0 C1 A:6NM1552 4.7 25.8 1.0 N19 A:6NM1552 4.8 35.8 1.0 C2 A:6NM1552 4.9 26.2 1.0 CG A:LEU408 4.9 22.1 1.0 C11 A:6NM1552 4.9 30.1 1.0

L.Oster, S.Tapani, Y.Xue, H.Kack. Successful Generation of Structural Information For Fragment-Based Drug Discovery. Drug Discov Today 2015.
ISSN: ESSN 1878-5832
PubMed: 25931264
DOI: 10.1016/J.DRUDIS.2015.04.005