Fluorine in PDB 6rnu: Bcl-Xl in A Complex with A Covalent Small Molecule Inhibitor

The structure of Bcl-Xl in A Complex with A Covalent Small Molecule Inhibitor, PDB code: 6rnu was solved by D.Hargreaves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.20 / 2.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.590, 96.590, 86.400, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 27.5

The structure of Bcl-Xl in A Complex with A Covalent Small Molecule Inhibitor also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Fluorine atom in the Bcl-Xl in A Complex with A Covalent Small Molecule Inhibitor (pdb code 6rnu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Bcl-Xl in A Complex with A Covalent Small Molecule Inhibitor, PDB code: 6rnu:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Bcl-Xl in A Complex with A Covalent Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Bcl-Xl in A Complex with A Covalent Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:54.4 occ:0.75 F A:KBH301 0.0 54.4 0.8 C8 A:KBH301 1.4 51.5 0.8 C9 A:KBH301 2.3 48.8 0.8 C7 A:KBH301 2.3 51.2 0.8 CZ B:PHE97 3.0 57.6 1.0 N B:PHE105 3.0 62.6 1.0 CA B:PHE105 3.1 62.5 1.0 CB B:PHE105 3.3 64.5 1.0 C B:ALA104 3.3 65.2 1.0 C10 A:KBH301 3.6 50.3 0.8 C6 A:KBH301 3.6 52.8 0.8 CE1 B:PHE97 3.6 59.4 1.0 CB B:ALA104 3.7 61.3 1.0 O B:ALA104 3.7 62.8 1.0 CD1 B:PHE105 3.8 70.5 1.0 CB B:TYR101 3.8 55.6 1.0 CE2 B:PHE97 3.9 59.4 1.0 CG B:PHE105 4.0 67.2 1.0 C5 A:KBH301 4.1 54.5 0.8 CA B:ALA104 4.1 61.1 1.0 O B:TYR101 4.2 64.7 1.0 CG B:TYR101 4.5 54.4 1.0 C B:PHE105 4.5 65.7 1.0 CD1 B:PHE97 4.9 58.4 1.0 CE1 B:PHE105 5.0 71.8 1.0

Fluorine binding site 2 out of 2 in the Bcl-Xl in A Complex with A Covalent Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Bcl-Xl in A Complex with A Covalent Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:55.4 occ:0.75 F A:KBH302 0.0 55.4 0.8 C8 A:KBH302 1.3 48.8 0.8 C9 A:KBH302 2.3 48.1 0.8 C7 A:KBH302 2.3 48.8 0.8 N A:PHE105 3.1 36.6 1.0 CA A:PHE105 3.2 35.5 1.0 CZ A:PHE97 3.2 33.6 1.0 C A:ALA104 3.4 42.3 1.0 CB A:PHE105 3.5 36.0 1.0 CB A:ALA104 3.6 43.5 1.0 C10 A:KBH302 3.6 53.1 0.8 C6 A:KBH302 3.6 51.5 0.8 CE1 A:PHE97 3.6 35.6 1.0 CB A:TYR101 3.8 40.9 1.0 O A:ALA104 3.8 43.0 1.0 O A:TYR101 4.0 41.6 1.0 CA A:ALA104 4.1 42.4 1.0 C5 A:KBH302 4.1 57.9 0.8 CD1 A:PHE105 4.3 37.5 1.0 CG A:PHE105 4.3 37.5 1.0 CE2 A:PHE97 4.4 35.8 1.0 CG A:TYR101 4.6 45.1 1.0 C A:PHE105 4.7 41.6 1.0 O A:HOH405 4.7 52.9 1.0 N A:ALA104 4.9 44.0 1.0 C A:TYR101 4.9 42.3 1.0 CD1 A:PHE97 4.9 36.0 1.0 CA A:TYR101 5.0 39.5 1.0

H.Mukherjee, N.Su, M.A.Belmonte, D.Hargreaves, J.Patel, S.Tentarelli, B.Aquila, N.P.Grimster. Discovery and Optimization of Covalent Bcl-Xl Antagonists. Bioorg.Med.Chem.Lett. V. 29 26682 2019.
ISSN: ESSN 1464-3405
PubMed: 31606346
DOI: 10.1016/J.BMCL.2019.126682