Fluorine in PDB 4c52: Crystal Structure of Bcl-Xl in Complex with Benzoylurea Compound (39B)

The structure of Crystal Structure of Bcl-Xl in Complex with Benzoylurea Compound (39B), PDB code: 4c52 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)	42.481 / 2.05
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	63.814, 63.814, 132.830, 90.00, 90.00, 120.00
R / Rfree (%)	15.9 / 21.57

The binding sites of Fluorine atom in the Crystal Structure of Bcl-Xl in Complex with Benzoylurea Compound (39B) (pdb code 4c52). 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 (39B), PDB code: 4c52:
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 (39B)


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 (39B) within 5.0Å range: probe atom residue distance (Å) B Occ A:F300 b:24.3 occ:1.00 F4 A:X0D300 0.0 24.3 1.0 C4 A:X0D300 1.4 25.7 1.0 C3 A:X0D300 2.4 25.2 1.0 C5 A:X0D300 2.4 23.6 1.0 CE2 A:PHE123 3.2 23.5 1.0 CZ A:PHE123 3.3 25.5 1.0 CA A:GLY147 3.4 15.2 1.0 C2 A:X0D300 3.6 27.3 1.0 C6 A:X0D300 3.7 21.0 1.0 CG A:MET170 3.8 18.9 1.0 N A:GLY147 4.0 23.0 1.0 SD A:MET170 4.0 21.2 1.0 CD1 A:LEU150 4.1 26.5 1.0 C1 A:X0D300 4.2 24.9 1.0 CG2 A:ILE166 4.3 17.7 1.0 CD2 A:PHE123 4.4 21.1 1.0 O A:PHE143 4.5 18.3 1.0 CE1 A:PHE123 4.7 16.8 1.0 C A:GLY147 4.7 26.9 1.0 C A:PHE146 4.7 26.4 1.0 F2 A:X0D300 4.7 41.9 1.0 CE A:MET170 4.8 16.8 1.0 CG2 A:VAL127 4.8 19.3 1.0 O A:PHE146 5.0 32.8 1.0 CE1 A:PHE143 5.0 20.0 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Bcl-Xl in Complex with Benzoylurea Compound (39B)


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 (39B) within 5.0Å range: probe atom residue distance (Å) B Occ A:F300 b:41.9 occ:1.00 F2 A:X0D300 0.0 41.9 1.0 C2 A:X0D300 1.3 27.3 1.0 C1 A:X0D300 2.3 24.9 1.0 C3 A:X0D300 2.4 25.2 1.0 C7 A:X0D300 2.6 27.8 1.0 C8 A:X0D300 3.3 25.1 1.0 CA A:PHE143 3.4 23.7 1.0 CB A:PHE146 3.5 15.9 1.0 CD2 A:LEU130 3.5 26.6 1.0 C6 A:X0D300 3.6 21.0 1.0 C4 A:X0D300 3.6 25.7 1.0 O A:PHE143 3.7 18.3 1.0 CD2 A:PHE146 3.7 26.4 1.0 C A:PHE143 4.0 24.9 1.0 CD1 A:PHE143 4.0 21.5 1.0 CG A:PHE146 4.1 23.1 1.0 C5 A:X0D300 4.1 23.6 1.0 O A:ALA142 4.1 23.6 1.0 CB A:PHE143 4.1 16.2 1.0 N A:PHE143 4.2 25.7 1.0 C9 A:X0D300 4.4 31.5 1.0 CG2 A:VAL127 4.4 19.3 1.0 CG A:PHE143 4.4 21.4 1.0 C A:ALA142 4.5 22.5 1.0 CA A:PHE146 4.7 25.5 1.0 F4 A:X0D300 4.7 24.3 1.0 N A:GLY147 4.8 23.0 1.0 C10 A:X0D300 4.8 25.6 1.0 CG A:LEU130 4.8 27.6 1.0 CG1 A:VAL127 4.8 21.6 1.0 CE2 A:PHE146 4.9 27.0 1.0 CB A:LEU130 4.9 20.9 1.0 C A:PHE146 5.0 26.4 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Bcl-Xl in Complex with Benzoylurea Compound (39B)


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 (39B) within 5.0Å range: probe atom residue distance (Å) B Occ B:F300 b:21.9 occ:1.00 F4 B:X0D300 0.0 21.9 1.0 C4 B:X0D300 1.3 19.7 1.0 C3 B:X0D300 2.3 18.2 1.0 C5 B:X0D300 2.4 18.0 1.0 CG B:MET170 3.3 13.9 1.0 CE2 B:PHE123 3.3 20.0 1.0 CZ B:PHE123 3.3 19.3 1.0 CA B:GLY147 3.4 16.9 1.0 SD B:MET170 3.6 21.2 1.0 C2 B:X0D300 3.6 19.0 1.0 C6 B:X0D300 3.6 19.1 1.0 CG2 B:ILE166 3.8 16.6 1.0 N B:GLY147 4.0 17.2 1.0 C1 B:X0D300 4.1 25.6 1.0 CE B:MET170 4.5 18.5 1.0 CD2 B:PHE123 4.6 22.1 1.0 CE1 B:PHE123 4.6 25.7 1.0 O B:PHE143 4.6 21.3 1.0 C B:GLY147 4.7 25.4 1.0 F2 B:X0D300 4.7 29.0 1.0 CE1 B:PHE143 4.7 22.8 1.0 CB B:MET170 4.8 18.7 1.0 CG2 B:VAL127 4.9 21.0 1.0 C B:PHE146 4.9 18.2 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Bcl-Xl in Complex with Benzoylurea Compound (39B)


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 (39B) within 5.0Å range: probe atom residue distance (Å) B Occ B:F300 b:29.0 occ:1.00 F2 B:X0D300 0.0 29.0 1.0 C2 B:X0D300 1.3 19.0 1.0 C1 B:X0D300 2.3 25.6 1.0 C3 B:X0D300 2.4 18.2 1.0 C7 B:X0D300 2.7 26.0 1.0 CA B:PHE143 3.3 19.2 1.0 CD2 B:LEU130 3.3 20.1 1.0 O B:PHE143 3.4 21.3 1.0 C8 B:X0D300 3.4 22.7 1.0 CB B:PHE146 3.5 14.6 1.0 C6 B:X0D300 3.6 19.1 1.0 C4 B:X0D300 3.6 19.7 1.0 CD1 B:PHE143 3.7 16.2 1.0 C B:PHE143 3.8 22.3 1.0 CB B:PHE143 4.0 14.2 1.0 C5 B:X0D300 4.1 18.0 1.0 O B:ALA142 4.2 21.7 1.0 N B:PHE143 4.2 20.3 1.0 CG B:PHE143 4.3 17.9 1.0 CD2 B:PHE146 4.3 14.5 1.0 CG B:PHE146 4.3 16.6 1.0 CG1 B:VAL127 4.3 17.4 1.0 CG2 B:VAL127 4.5 21.0 1.0 C9 B:X0D300 4.5 24.3 1.0 N B:GLY147 4.5 17.2 1.0 C B:ALA142 4.6 20.5 1.0 CA B:PHE146 4.6 19.8 1.0 CG B:LEU130 4.6 20.9 1.0 CE1 B:PHE143 4.6 22.8 1.0 F4 B:X0D300 4.7 21.9 1.0 CB B:LEU130 4.8 19.1 1.0 C B:PHE146 4.8 18.2 1.0 CB B:VAL127 4.9 18.2 1.0 N B:PHE146 5.0 18.5 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