Fluorine in PDB 5ye8: The Crystal Structure of Lp-PLA2 in Complex with A Novel Inhibitor

All present enzymatic activity of The Crystal Structure of Lp-PLA2 in Complex with A Novel Inhibitor:
3.1.1.47;

The structure of The Crystal Structure of Lp-PLA2 in Complex with A Novel Inhibitor, PDB code: 5ye8 was solved by Q.F.Liu, Y.C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.73 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.869, 82.772, 96.655, 90.00, 115.25, 90.00
R / Rfree (%)	18.1 / 21.2

The binding sites of Fluorine atom in the The Crystal Structure of Lp-PLA2 in Complex with A Novel Inhibitor (pdb code 5ye8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the The Crystal Structure of Lp-PLA2 in Complex with A Novel Inhibitor, PDB code: 5ye8:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the The Crystal Structure of Lp-PLA2 in Complex with A Novel Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Crystal Structure of Lp-PLA2 in Complex with A Novel Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:21.6 occ:1.00 F7 B:8U3501 0.0 21.6 1.0 C6 B:8U3501 1.3 15.6 1.0 C8 B:8U3501 2.3 19.6 1.0 C5 B:8U3501 2.4 16.9 1.0 F9 B:8U3501 2.7 17.8 1.0 CB B:ALA355 3.4 12.0 1.0 OE1 B:GLN352 3.5 20.6 1.0 C10 B:8U3501 3.6 15.8 1.0 C4 B:8U3501 3.6 15.3 1.0 CD2 B:PHE357 3.7 16.1 1.0 O B:HOH694 3.9 17.0 1.0 CD1 B:LEU159 3.9 12.4 1.0 C11 B:8U3501 4.1 14.3 1.0 CB B:LEU159 4.4 10.6 1.0 CB B:PHE357 4.4 13.9 1.0 CG B:PHE357 4.5 20.0 1.0 CE2 B:PHE357 4.5 15.5 1.0 N B:PHE357 4.6 14.2 1.0 CD B:GLN352 4.6 20.3 1.0 CG B:LEU159 4.7 15.6 1.0 CA B:ALA355 4.7 13.3 1.0 N B:ASP356 4.8 15.5 1.0 N3 B:8U3501 4.8 18.8 1.0 O13 B:8U3501 4.8 15.6 1.0 C B:ALA355 4.9 13.2 1.0 O B:LEU159 4.9 11.4 1.0

Fluorine binding site 2 out of 4 in the The Crystal Structure of Lp-PLA2 in Complex with A Novel Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Crystal Structure of Lp-PLA2 in Complex with A Novel Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:17.8 occ:1.00 F9 B:8U3501 0.0 17.8 1.0 C8 B:8U3501 1.3 19.6 1.0 C10 B:8U3501 2.4 15.8 1.0 C6 B:8U3501 2.4 15.6 1.0 F7 B:8U3501 2.7 21.6 1.0 CD2 B:PHE357 3.1 16.1 1.0 CE2 B:PHE357 3.2 15.5 1.0 CD1 B:LEU159 3.5 12.4 1.0 CD2 B:LEU107 3.5 14.6 1.0 C11 B:8U3501 3.6 14.3 1.0 C5 B:8U3501 3.6 16.9 1.0 C4 B:8U3501 4.1 15.3 1.0 CG B:PHE357 4.2 20.0 1.0 CZ B:PHE357 4.4 16.8 1.0 CD1 B:LEU107 4.8 17.8 1.0 CG B:LEU107 4.8 17.2 1.0 CG B:LEU159 4.8 15.6 1.0 CB B:PHE357 4.9 13.9 1.0 O B:GLY154 5.0 12.0 1.0

Fluorine binding site 3 out of 4 in the The Crystal Structure of Lp-PLA2 in Complex with A Novel Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Crystal Structure of Lp-PLA2 in Complex with A Novel Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:21.8 occ:1.00 F7 A:8U3501 0.0 21.8 1.0 C6 A:8U3501 1.3 17.8 1.0 C8 A:8U3501 2.3 16.9 1.0 C5 A:8U3501 2.4 19.1 1.0 F9 A:8U3501 2.7 19.6 1.0 CB A:ALA355 3.4 16.1 1.0 OE1 A:GLN352 3.4 23.0 1.0 C10 A:8U3501 3.6 16.5 1.0 C4 A:8U3501 3.6 15.5 1.0 CD2 A:PHE357 3.6 14.6 1.0 O A:HOH616 3.8 18.8 1.0 CD1 A:LEU159 3.9 15.3 1.0 C11 A:8U3501 4.1 15.1 1.0 CB A:LEU159 4.3 12.2 1.0 CB A:PHE357 4.4 19.1 1.0 CG A:PHE357 4.5 19.4 1.0 CE2 A:PHE357 4.5 19.6 1.0 CD A:GLN352 4.5 20.3 1.0 N A:PHE357 4.6 14.1 1.0 CG A:LEU159 4.6 14.0 1.0 CA A:ALA355 4.7 14.6 1.0 N A:ASP356 4.7 15.0 1.0 N3 A:8U3501 4.8 15.3 1.0 O13 A:8U3501 4.9 18.0 1.0 C A:ALA355 4.9 17.2 1.0 NE2 A:GLN352 5.0 17.7 1.0 O A:LEU159 5.0 15.8 1.0

Fluorine binding site 4 out of 4 in the The Crystal Structure of Lp-PLA2 in Complex with A Novel Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Crystal Structure of Lp-PLA2 in Complex with A Novel Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:19.6 occ:1.00 F9 A:8U3501 0.0 19.6 1.0 C8 A:8U3501 1.3 16.9 1.0 C6 A:8U3501 2.3 17.8 1.0 C10 A:8U3501 2.4 16.5 1.0 F7 A:8U3501 2.7 21.8 1.0 CD2 A:PHE357 3.0 14.6 1.0 CE2 A:PHE357 3.1 19.6 1.0 CD2 A:LEU107 3.5 15.3 1.0 CD1 A:LEU159 3.6 15.3 1.0 C11 A:8U3501 3.6 15.1 1.0 C5 A:8U3501 3.6 19.1 1.0 C4 A:8U3501 4.1 15.5 1.0 CG A:PHE357 4.1 19.4 1.0 CZ A:PHE357 4.3 19.3 1.0 CD1 A:LEU107 4.7 14.5 1.0 CG A:LEU107 4.7 18.1 1.0 CB A:PHE357 4.8 19.1 1.0 CG A:LEU159 4.8 14.0 1.0 CD2 A:LEU159 4.9 13.9 1.0 OE1 A:GLN352 4.9 23.0 1.0

Q.Liu, F.Huang, X.Yuan, K.Wang, Y.Zou, J.Shen, Y.Xu. Structure-Guided Discovery of Novel, Potent, and Orally Bioavailable Inhibitors of Lipoprotein-Associated Phospholipase A2. J. Med. Chem. V. 60 10231 2017.
ISSN: ISSN 1520-4804
PubMed: 29193967
DOI: 10.1021/ACS.JMEDCHEM.7B01530