Fluorine in PDB 4c5d: Crystal Structure of Bcl-Xl in Complex with Benzoylurea Compound (42)

The structure of Crystal Structure of Bcl-Xl in Complex with Benzoylurea Compound (42), PDB code: 4c5d was solved by M.J.Roy, R.M.Brady, G.Lessene, P.M.Colman, P.E.Czabotar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.125 / 2.30
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	64.138, 64.138, 132.376, 90.00, 90.00, 120.00
R / Rfree (%)	16.61 / 24.16

The structure of Crystal Structure of Bcl-Xl in Complex with Benzoylurea Compound (42) also contains other interesting chemical elements:

Bromine

(Br)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Bcl-Xl in Complex with Benzoylurea Compound (42) (pdb code 4c5d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Bcl-Xl in Complex with Benzoylurea Compound (42), PDB code: 4c5d:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Bcl-Xl in Complex with Benzoylurea Compound (42)


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 Bcl-Xl in Complex with Benzoylurea Compound (42) within 5.0Å range: probe atom residue distance (Å) B Occ A:F2000 b:28.7 occ:1.00 F4 A:X0R2000 0.0 28.7 1.0 C4 A:X0R2000 1.4 24.7 1.0 C3 A:X0R2000 2.4 23.1 1.0 C5 A:X0R2000 2.4 27.7 1.0 CE2 A:PHE123 3.1 28.3 1.0 CZ A:PHE123 3.4 21.2 1.0 CA A:GLY147 3.4 18.9 1.0 CG A:MET170 3.5 18.1 1.0 C2 A:X0R2000 3.6 30.4 1.0 C6 A:X0R2000 3.7 24.2 1.0 SD A:MET170 3.9 21.1 1.0 N A:GLY147 4.0 21.6 1.0 CD1 A:LEU150 4.2 31.4 1.0 C1 A:X0R2000 4.2 24.7 1.0 CG2 A:ILE166 4.2 25.0 1.0 CD2 A:PHE123 4.3 24.3 1.0 O A:PHE143 4.6 23.7 1.0 CE A:MET170 4.7 20.1 1.0 F2 A:X0R2000 4.7 43.2 1.0 CE1 A:PHE123 4.7 26.4 1.0 CE1 A:PHE143 4.7 27.9 1.0 C A:GLY147 4.7 30.3 1.0 C A:PHE146 4.8 20.8 1.0 CG2 A:VAL127 4.8 26.2 1.0 CB A:MET170 4.9 21.2 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Bcl-Xl in Complex with Benzoylurea Compound (42)


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 Bcl-Xl in Complex with Benzoylurea Compound (42) within 5.0Å range: probe atom residue distance (Å) B Occ A:F2000 b:43.2 occ:1.00 F2 A:X0R2000 0.0 43.2 1.0 C2 A:X0R2000 1.3 30.4 1.0 C3 A:X0R2000 2.3 23.1 1.0 C1 A:X0R2000 2.4 24.7 1.0 C7 A:X0R2000 2.7 28.5 1.0 CA A:PHE143 3.3 18.6 1.0 C8 A:X0R2000 3.5 31.1 1.0 CB A:PHE146 3.5 20.0 1.0 CD2 A:LEU130 3.5 19.9 1.0 O A:PHE143 3.6 23.7 1.0 C4 A:X0R2000 3.6 24.7 1.0 C6 A:X0R2000 3.6 24.2 1.0 CD1 A:PHE143 3.8 18.8 1.0 CD2 A:PHE146 3.9 31.6 1.0 C A:PHE143 3.9 20.4 1.0 CB A:PHE143 4.0 18.4 1.0 O A:ALA142 4.1 35.0 1.0 C5 A:X0R2000 4.1 27.7 1.0 N A:PHE143 4.1 21.7 1.0 CG A:PHE146 4.1 24.2 1.0 CG A:PHE143 4.3 23.0 1.0 C A:ALA142 4.4 23.7 1.0 C9 A:X0R2000 4.5 37.1 1.0 CG2 A:VAL127 4.5 26.2 1.0 CA A:PHE146 4.7 26.1 1.0 F4 A:X0R2000 4.7 28.7 1.0 CG A:LEU130 4.7 29.7 1.0 CE1 A:PHE143 4.8 27.9 1.0 CG1 A:VAL127 4.8 19.1 1.0 N A:GLY147 4.8 21.6 1.0 CB A:LEU130 4.9 30.0 1.0 C10 A:X0R2000 5.0 36.9 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Bcl-Xl in Complex with Benzoylurea Compound (42)


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 Bcl-Xl in Complex with Benzoylurea Compound (42) within 5.0Å range: probe atom residue distance (Å) B Occ B:F2000 b:22.9 occ:1.00 F4 B:X0R2000 0.0 22.9 1.0 C4 B:X0R2000 1.4 24.0 1.0 C3 B:X0R2000 2.4 25.1 1.0 C5 B:X0R2000 2.4 25.8 1.0 CZ B:PHE123 3.3 18.1 1.0 CG B:MET170 3.3 17.4 1.0 CE2 B:PHE123 3.4 23.6 1.0 CA B:GLY147 3.5 20.2 1.0 C2 B:X0R2000 3.6 30.0 1.0 C6 B:X0R2000 3.7 25.4 1.0 SD B:MET170 3.7 24.6 1.0 N B:GLY147 4.1 20.0 1.0 CG2 B:ILE166 4.1 18.6 1.0 C1 B:X0R2000 4.2 29.8 1.0 CE1 B:PHE123 4.5 23.7 1.0 F2 B:X0R2000 4.7 38.0 1.0 CD2 B:PHE123 4.7 27.8 1.0 CE B:MET170 4.7 16.1 1.0 O B:PHE143 4.8 25.7 1.0 CE1 B:PHE143 4.8 16.4 1.0 C B:GLY147 4.8 24.8 1.0 CB B:MET170 4.8 23.1 1.0 CG2 B:VAL127 4.9 27.5 1.0 C B:PHE146 4.9 26.5 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Bcl-Xl in Complex with Benzoylurea Compound (42)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Bcl-Xl in Complex with Benzoylurea Compound (42) within 5.0Å range: probe atom residue distance (Å) B Occ B:F2000 b:38.0 occ:1.00 F2 B:X0R2000 0.0 38.0 1.0 C2 B:X0R2000 1.3 30.0 1.0 C3 B:X0R2000 2.3 25.1 1.0 C1 B:X0R2000 2.4 29.8 1.0 C7 B:X0R2000 2.8 23.6 1.0 CD2 B:LEU130 3.2 17.8 1.0 CA B:PHE143 3.2 16.8 1.0 O B:PHE143 3.3 25.7 1.0 CB B:PHE146 3.5 30.2 1.0 C8 B:X0R2000 3.6 28.1 1.0 C4 B:X0R2000 3.6 24.0 1.0 C6 B:X0R2000 3.6 25.4 1.0 CD1 B:PHE143 3.7 16.4 1.0 C B:PHE143 3.8 22.8 1.0 CB B:PHE143 3.8 16.5 1.0 C5 B:X0R2000 4.1 25.8 1.0 CG B:PHE143 4.1 16.8 1.0 CG1 B:VAL127 4.2 29.4 1.0 N B:PHE143 4.3 21.4 1.0 CD2 B:PHE146 4.3 22.0 1.0 O B:ALA142 4.3 26.8 1.0 CG B:PHE146 4.3 21.2 1.0 CG B:LEU130 4.5 23.4 1.0 CE1 B:PHE143 4.6 16.4 1.0 C9 B:X0R2000 4.6 32.2 1.0 CG2 B:VAL127 4.6 27.5 1.0 N B:GLY147 4.6 20.0 1.0 C B:ALA142 4.6 25.4 1.0 F4 B:X0R2000 4.7 22.9 1.0 CA B:PHE146 4.7 23.5 1.0 CB B:LEU130 4.8 24.2 1.0 CB B:VAL127 4.9 28.6 1.0 C B:PHE146 4.9 26.5 1.0

R.M.Brady, A.Vom, M.J.Roy, N.Toovey, B.J.Smith, R.M.Moss, E.Hazis, D.C.S.Huang, J.P.Parisot, H.Yang, I.P.Street, P.M.Colman, P.E.Czabotar, J.B.Baell, G.Lessene. De-Novo Designed Library of Benzoylureas As Inhibitors of Bcl-Xl: Synthesis, Structural and Biochemical Characterization. J.Med.Chem. V. 57 1323 2014.
ISSN: ISSN 0022-2623
PubMed: 24456288
DOI: 10.1021/JM401948B