Fluorine in PDB 6lqg: Human Gamma-Secretase in Complex with Small Molecule Avagacestat

The structure of Human Gamma-Secretase in Complex with Small Molecule Avagacestat also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Human Gamma-Secretase in Complex with Small Molecule Avagacestat (pdb code 6lqg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Human Gamma-Secretase in Complex with Small Molecule Avagacestat, PDB code: 6lqg:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Human Gamma-Secretase in Complex with Small Molecule Avagacestat


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Gamma-Secretase in Complex with Small Molecule Avagacestat within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:86.9 occ:1.00 F03 B:EN9701 0.0 86.9 1.0 C22 B:EN9701 1.3 86.9 1.0 F04 B:EN9701 2.1 86.9 1.0 F05 B:EN9701 2.1 86.9 1.0 C18 B:EN9701 2.4 86.9 1.0 C16 B:EN9701 2.7 86.9 1.0 C15 B:EN9701 3.2 86.9 1.0 CG2 B:VAL272 3.3 83.2 1.0 F06 B:EN9701 3.3 86.9 1.0 N11 B:EN9701 4.1 86.9 1.0 CB B:ALA431 4.3 78.3 1.0 C19 B:EN9701 4.4 86.9 1.0 O08 B:EN9701 4.6 86.9 1.0 C23 B:EN9701 4.6 86.9 1.0 CB B:VAL272 4.7 83.2 1.0 N12 B:EN9701 4.7 86.9 1.0 O B:LEU268 4.7 82.2 1.0 C17 B:EN9701 4.8 86.9 1.0

Fluorine binding site 2 out of 4 in the Human Gamma-Secretase in Complex with Small Molecule Avagacestat


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Gamma-Secretase in Complex with Small Molecule Avagacestat within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:86.9 occ:1.00 F04 B:EN9701 0.0 86.9 1.0 C22 B:EN9701 1.3 86.9 1.0 F03 B:EN9701 2.1 86.9 1.0 F05 B:EN9701 2.1 86.9 1.0 C18 B:EN9701 2.4 86.9 1.0 CD2 B:LEU268 3.2 82.2 1.0 CB B:LEU268 3.3 82.2 1.0 C16 B:EN9701 3.6 86.9 1.0 CG B:LEU268 3.7 82.2 1.0 O B:LEU268 3.9 82.2 1.0 CG2 B:VAL272 4.0 83.2 1.0 C B:LEU268 4.2 82.2 1.0 CA B:LEU268 4.2 82.2 1.0 C15 B:EN9701 4.6 86.9 1.0 CG2 B:VAL261 4.6 78.4 1.0 F06 B:EN9701 5.0 86.9 1.0

Fluorine binding site 3 out of 4 in the Human Gamma-Secretase in Complex with Small Molecule Avagacestat


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Gamma-Secretase in Complex with Small Molecule Avagacestat within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:86.9 occ:1.00 F05 B:EN9701 0.0 86.9 1.0 C22 B:EN9701 1.3 86.9 1.0 F04 B:EN9701 2.1 86.9 1.0 F03 B:EN9701 2.1 86.9 1.0 C18 B:EN9701 2.4 86.9 1.0 C16 B:EN9701 3.4 86.9 1.0 C15 B:EN9701 3.6 86.9 1.0 N12 B:EN9701 3.6 86.9 1.0 CG2 B:VAL261 3.8 78.4 1.0 C19 B:EN9701 4.0 86.9 1.0 CD2 B:LEU268 4.3 82.2 1.0 CG1 B:VAL261 4.4 78.4 1.0 O B:LEU432 4.7 77.8 1.0 CB B:VAL261 4.7 78.4 1.0 CB B:LEU268 4.8 82.2 1.0 N11 B:EN9701 5.0 86.9 1.0

Fluorine binding site 4 out of 4 in the Human Gamma-Secretase in Complex with Small Molecule Avagacestat


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Gamma-Secretase in Complex with Small Molecule Avagacestat within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:86.9 occ:1.00 F06 B:EN9701 0.0 86.9 1.0 C23 B:EN9701 1.3 86.9 1.0 C27 B:EN9701 2.4 86.9 1.0 C20 B:EN9701 2.4 86.9 1.0 C17 B:EN9701 3.0 86.9 1.0 C16 B:EN9701 3.2 86.9 1.0 F03 B:EN9701 3.3 86.9 1.0 N11 B:EN9701 3.4 86.9 1.0 CG2 B:VAL272 3.5 83.2 1.0 C24 B:EN9701 3.6 86.9 1.0 C29 B:EN9701 3.7 86.9 1.0 C15 B:EN9701 3.7 86.9 1.0 C28 B:EN9701 4.1 86.9 1.0 O08 B:EN9701 4.2 86.9 1.0 C18 B:EN9701 4.2 86.9 1.0 C22 B:EN9701 4.3 86.9 1.0 S02 B:EN9701 4.3 86.9 1.0 CG1 B:VAL272 4.4 83.2 1.0 CD2 B:LEU282 4.5 84.3 1.0 CB B:VAL272 4.5 83.2 1.0 O07 B:EN9701 4.6 86.9 1.0 F04 B:EN9701 5.0 86.9 1.0

G.Yang, R.Zhou, X.Guo, C.Yan, J.Lei, Y.Shi. Structural Basis of Gamma-Secretase Inhibition and Modulation By Small Molecule Drugs. Cell 2020.
ISSN: ISSN 1097-4172
PubMed: 33373587
DOI: 10.1016/J.CELL.2020.11.049