Bromine 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:

Fluorine

(F)

4 atoms

The binding sites of Bromine 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 Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of Bcl-Xl in Complex with Benzoylurea Compound (42), PDB code: 4c5d:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of Bcl-Xl in Complex with Benzoylurea Compound (42)


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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:Br2000 b:56.4 occ:1.00 BR A:X0R2000 0.0 56.4 1.0 C28 A:X0R2000 1.9 38.0 1.0 C27 A:X0R2000 2.8 33.4 1.0 C29 A:X0R2000 2.9 38.6 1.0 O A:HOH2043 3.2 43.0 1.0 NE A:ARG139 3.8 51.9 1.0 C A:GLY138 3.9 29.2 1.0 N A:ARG139 3.9 40.0 1.0 O2 A:SO41198 3.9 74.1 1.0 CZ A:ARG139 4.0 48.3 1.0 O A:GLY138 4.0 33.2 1.0 CG A:ARG139 4.0 29.3 1.0 CD A:ARG139 4.1 40.6 1.0 C26 A:X0R2000 4.1 33.5 1.0 CA A:ARG139 4.1 30.6 1.0 C30 A:X0R2000 4.2 38.8 1.0 O1 A:SO41198 4.2 77.8 1.0 NH2 A:ARG139 4.4 44.8 1.0 CA A:GLY138 4.4 28.6 1.0 S A:SO41198 4.5 77.5 1.0 NH1 A:ARG139 4.5 43.1 1.0 C25 A:X0R2000 4.7 42.5 1.0 CB A:ARG139 4.7 26.7 1.0 O4 A:SO41198 4.8 81.5 1.0 CB A:ALA142 4.8 20.8 1.0 CE2 A:PHE97 4.9 30.3 1.0 OD1 A:ASN136 4.9 34.3 1.0

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


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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 B:Br2000 b:59.6 occ:1.00 BR B:X0R2000 0.0 59.6 1.0 C28 B:X0R2000 1.9 34.7 1.0 C29 B:X0R2000 2.9 30.4 1.0 C27 B:X0R2000 2.9 29.6 1.0 O B:HOH2027 3.4 46.1 1.0 O B:HOH2013 3.4 43.8 1.0 NE B:ARG139 3.6 39.4 1.0 CD B:ARG139 3.8 38.0 1.0 O B:GLY138 3.9 21.8 1.0 O B:HOH2030 3.9 45.3 1.0 C B:GLY138 3.9 23.8 1.0 CZ B:ARG139 4.0 39.4 1.0 O3 B:SO41199 4.0 51.3 1.0 N B:ARG139 4.0 26.5 1.0 CA B:ARG139 4.1 28.3 1.0 CG B:ARG139 4.1 30.9 1.0 C30 B:X0R2000 4.2 34.3 1.0 C26 B:X0R2000 4.2 27.5 1.0 NH2 B:ARG139 4.4 44.1 1.0 NH1 B:ARG139 4.5 29.1 1.0 O1 B:SO41199 4.5 43.7 1.0 CE2 B:PHE97 4.6 25.3 1.0 CB B:ALA142 4.6 19.0 1.0 S B:SO41199 4.6 49.0 1.0 CA B:GLY138 4.6 19.5 1.0 O2 B:SO41199 4.7 47.1 1.0 CB B:ARG139 4.7 29.2 1.0 C25 B:X0R2000 4.7 33.2 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