Fluorine in PDB 6m08: Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor.

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

The structure of Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor., PDB code: 6m08 was solved by H.C.Hu, Y.C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.39 / 2.19
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.346, 82.345, 96.664, 90, 115.73, 90
R / Rfree (%)	19.3 / 24

The binding sites of Fluorine atom in the Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor. (pdb code 6m08). 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 Lp-PLA2 in Complex with A Novel Covalent Inhibitor., PDB code: 6m08:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent 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 Lp-PLA2 in Complex with A Novel Covalent Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:72.5 occ:1.00 F15 B:BWL501 0.0 72.5 1.0 C14 B:BWL501 1.3 69.8 1.0 F18 B:BWL501 2.1 71.4 1.0 F17 B:BWL501 2.2 68.4 1.0 C11 B:BWL501 2.3 65.6 1.0 C12 B:BWL501 3.1 62.3 1.0 C10 B:BWL501 3.2 67.0 1.0 CD1 B:PHE357 3.3 33.2 1.0 CE1 B:PHE357 3.3 34.1 1.0 CD1 B:LEU371 3.7 33.5 1.0 CG B:PHE357 4.2 31.6 1.0 CE2 B:PHE125 4.2 37.6 1.0 CZ B:PHE357 4.3 37.1 1.0 C13 B:BWL501 4.4 62.4 1.0 CZ B:PHE125 4.4 37.7 1.0 C9 B:BWL501 4.4 66.0 1.0 CG2 B:THR361 4.7 52.9 1.0 CD2 B:LEU371 4.7 33.5 1.0 CD2 B:LEU121 4.8 35.9 1.0 CG B:LEU371 4.8 32.3 1.0 CB B:PHE357 4.8 29.4 1.0 CD1 B:LEU369 4.9 49.1 1.0 C8 B:BWL501 4.9 65.5 1.0 CD2 B:PHE357 4.9 33.6 1.0 CE2 B:PHE357 5.0 37.0 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent 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 Lp-PLA2 in Complex with A Novel Covalent Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:68.4 occ:1.00 F17 B:BWL501 0.0 68.4 1.0 C14 B:BWL501 1.3 69.8 1.0 F18 B:BWL501 2.2 71.4 1.0 F15 B:BWL501 2.2 72.5 1.0 C11 B:BWL501 2.3 65.6 1.0 C12 B:BWL501 2.7 62.3 1.0 CE1 B:PHE357 3.4 34.1 1.0 C10 B:BWL501 3.5 67.0 1.0 CD2 B:LEU121 3.6 35.9 1.0 CZ B:PHE357 3.6 37.1 1.0 CD1 B:PHE357 3.9 33.2 1.0 C13 B:BWL501 4.0 62.4 1.0 CD1 B:LEU111 4.2 36.7 1.0 CE2 B:PHE357 4.3 37.0 1.0 CD1 B:LEU121 4.3 37.9 1.0 CG B:LEU121 4.6 36.0 1.0 C9 B:BWL501 4.6 66.0 1.0 CG B:PHE357 4.6 31.6 1.0 CE2 B:PHE125 4.7 37.6 1.0 CD2 B:PHE357 4.8 33.6 1.0 C8 B:BWL501 4.8 65.5 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent 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 Lp-PLA2 in Complex with A Novel Covalent Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:71.4 occ:1.00 F18 B:BWL501 0.0 71.4 1.0 C14 B:BWL501 1.3 69.8 1.0 F15 B:BWL501 2.1 72.5 1.0 F17 B:BWL501 2.2 68.4 1.0 C11 B:BWL501 2.3 65.6 1.0 C10 B:BWL501 2.7 67.0 1.0 C12 B:BWL501 3.6 62.3 1.0 CD2 B:LEU121 3.8 35.9 1.0 C9 B:BWL501 4.0 66.0 1.0 CD1 B:LEU111 4.3 36.7 1.0 CD1 B:LEU369 4.5 49.1 1.0 C13 B:BWL501 4.7 62.4 1.0 C8 B:BWL501 4.9 65.5 1.0 CE2 B:PHE125 5.0 37.6 1.0 CE1 B:PHE357 5.0 34.1 1.0

F.Huang, H.Hu, K.Wang, C.Peng, W.Xu, Y.Zhang, J.Gao, Y.Liu, H.Zhou, R.Huang, M.Li, J.Shen, Y.Xu. Identification of Highly Selective Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Inhibitors By A Covalent Fragment-Based Approach. J.Med.Chem. V. 63 7052 2020.
ISSN: ISSN 0022-2623
PubMed: 32459096
DOI: 10.1021/ACS.JMEDCHEM.0C00372