Bromine in PDB 3lbz: Crystal Structure of the BCL6 Btb Domain Complexed with the Small Molecule Inhibitor 79-6

The structure of Crystal Structure of the BCL6 Btb Domain Complexed with the Small Molecule Inhibitor 79-6, PDB code: 3lbz was solved by A.F.Ghetu, G.G.Prive, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.23 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.712, 38.611, 78.817, 90.00, 114.70, 90.00
R / Rfree (%)	21.3 / 26.9

The binding sites of Bromine atom in the Crystal Structure of the BCL6 Btb Domain Complexed with the Small Molecule Inhibitor 79-6 (pdb code 3lbz). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 5 binding sites of Bromine where determined in the Crystal Structure of the BCL6 Btb Domain Complexed with the Small Molecule Inhibitor 79-6, PDB code: 3lbz:
Jump to Bromine binding site number: 1; 2; 3; 4; 5;

Bromine binding site 1 out of 5 in the Crystal Structure of the BCL6 Btb Domain Complexed with the Small Molecule Inhibitor 79-6


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 the BCL6 Btb Domain Complexed with the Small Molecule Inhibitor 79-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br200 b:86.7 occ:1.00 BRAE A:Z88200 0.0 86.7 1.0 CAL A:Z88200 1.9 81.9 1.0 CAG A:Z88200 2.9 81.4 1.0 CAF A:Z88200 3.0 79.4 1.0 CAI A:Z88200 4.2 81.0 1.0 CAH A:Z88200 4.2 80.3 1.0 BRAE B:Z88200 4.3 83.7 1.0 CG1 A:ILE9 4.5 42.9 1.0 CE1 B:PHE124 4.6 35.1 1.0 CAG B:Z88200 4.7 77.1 1.0 CAM A:Z88200 4.7 80.6 1.0 CD1 A:ILE9 4.8 38.8 1.0 CD1 B:PHE124 4.8 36.5 1.0

Bromine binding site 2 out of 5 in the Crystal Structure of the BCL6 Btb Domain Complexed with the Small Molecule Inhibitor 79-6


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 the BCL6 Btb Domain Complexed with the Small Molecule Inhibitor 79-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br201 b:91.6 occ:0.80 BRAE A:Z89201 0.0 91.6 0.8 CAD A:Z89201 1.9 91.8 0.8 CAF A:Z89201 2.9 91.7 0.8 CAC A:Z89201 2.9 91.7 0.8 NH1 A:ARG28 3.1 70.3 1.0 CE1 B:TYR58 3.6 35.9 1.0 CD A:ARG28 3.6 57.5 1.0 CZ A:ARG28 3.6 73.0 1.0 CB A:ARG24 3.7 34.4 1.0 NE A:ARG28 3.8 66.1 1.0 OH B:TYR58 3.8 41.7 1.0 N A:LEU25 3.9 31.6 1.0 C A:ARG24 3.9 32.3 1.0 CD2 A:LEU25 4.0 30.0 1.0 CZ B:TYR58 4.0 37.4 1.0 O A:ARG24 4.1 33.2 1.0 OAZ A:Z89201 4.2 92.0 0.8 CAG A:Z89201 4.2 91.7 0.8 CAB A:Z89201 4.2 91.7 0.8 CA A:LEU25 4.4 30.0 1.0 CA A:ARG24 4.5 33.7 1.0 CD1 B:TYR58 4.5 36.2 1.0 NE A:ARG24 4.5 53.6 1.0 NH2 A:ARG28 4.6 74.0 1.0 CG A:LEU25 4.6 32.0 1.0 CD1 A:ILE30 4.6 33.5 1.0 CAA A:Z89201 4.8 91.5 0.8 CZ A:ARG24 4.8 62.0 1.0 NH2 A:ARG24 4.9 59.6 1.0 O A:ASN21 4.9 29.6 1.0 CG A:ARG28 5.0 46.9 1.0 CG A:ARG24 5.0 39.5 1.0

Bromine binding site 3 out of 5 in the Crystal Structure of the BCL6 Btb Domain Complexed with the Small Molecule Inhibitor 79-6


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of the BCL6 Btb Domain Complexed with the Small Molecule Inhibitor 79-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br202 b:90.0 occ:0.70 BRAE A:Z89202 0.0 90.0 0.7 CAD A:Z89202 1.9 89.5 0.7 CAF A:Z89202 2.8 89.5 0.7 CAC A:Z89202 2.9 89.5 0.7 NH1 B:ARG28 3.5 74.2 1.0 CB B:ARG24 3.6 34.9 1.0 CE1 A:TYR58 3.7 34.8 1.0 CD2 B:LEU25 3.9 31.4 1.0 CZ B:ARG28 3.9 74.2 1.0 OAZ A:Z89202 4.0 89.7 0.7 N B:LEU25 4.0 32.8 1.0 C B:ARG24 4.1 33.1 1.0 OH A:TYR58 4.1 41.0 1.0 CZ A:TYR58 4.2 36.1 1.0 CAB A:Z89202 4.2 89.8 0.7 CAG A:Z89202 4.2 89.6 0.7 NE B:ARG28 4.2 67.8 1.0 CD B:ARG28 4.3 59.4 1.0 O B:ARG24 4.3 33.5 1.0 NE B:ARG24 4.5 56.2 1.0 CA B:LEU25 4.5 31.4 1.0 CA B:ARG24 4.5 34.0 1.0 CD1 A:TYR58 4.6 35.0 1.0 NH2 B:ARG28 4.7 74.2 1.0 CAA A:Z89202 4.7 89.6 0.7 CG B:LEU25 4.8 35.2 1.0 CZ B:ARG24 4.8 62.4 1.0 CG B:ARG24 4.8 42.3 1.0 O B:ASN21 4.8 30.7 1.0 CD1 B:ILE30 4.9 35.4 1.0 CD B:ARG24 4.9 41.9 1.0

Bromine binding site 4 out of 5 in the Crystal Structure of the BCL6 Btb Domain Complexed with the Small Molecule Inhibitor 79-6


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of the BCL6 Btb Domain Complexed with the Small Molecule Inhibitor 79-6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br200 b:83.7 occ:1.00 BRAE B:Z88200 0.0 83.7 1.0 CAL B:Z88200 1.9 78.5 1.0 CAG B:Z88200 2.8 77.1 1.0 CAF B:Z88200 2.9 76.3 1.0 CB B:ALA127 3.9 48.2 1.0 CA B:PHE124 4.0 36.0 1.0 CAI B:Z88200 4.1 77.0 1.0 CAH B:Z88200 4.2 76.8 1.0 CD1 B:PHE124 4.3 36.5 1.0 O B:LYS123 4.3 35.7 1.0 N B:PHE124 4.3 35.6 1.0 BRAE A:Z88200 4.3 86.7 1.0 CB B:PHE124 4.5 34.9 1.0 C B:LYS123 4.5 34.6 1.0 CAM B:Z88200 4.7 76.5 1.0 CAG A:Z88200 4.7 81.4 1.0 CG B:PHE124 4.7 35.9 1.0

Bromine binding site 5 out of 5 in the Crystal Structure of the BCL6 Btb Domain Complexed with the Small Molecule Inhibitor 79-6


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of the BCL6 Btb Domain Complexed with the Small Molecule Inhibitor 79-6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br203 b:70.9 occ:0.92 BRAE B:Z89203 0.0 70.9 0.9 CAD B:Z89203 1.9 68.7 0.9 CAC B:Z89203 2.9 68.0 0.9 CAF B:Z89203 2.9 68.2 0.9 CD B:PRO76 4.1 47.8 1.0 CAB B:Z89203 4.2 68.5 0.9 CAG B:Z89203 4.2 68.4 0.9 CG B:PRO76 4.5 49.3 1.0 CAA B:Z89203 4.7 68.4 0.9 OAZ B:Z89203 4.7 67.9 0.9

L.C.Cerchietti, A.F.Ghetu, X.Zhu, G.F.Da Silva, S.Zhong, M.Matthews, K.L.Bunting, J.M.Polo, C.Fares, C.H.Arrowsmith, S.N.Yang, M.Garcia, A.Coop, A.D.Mackerell, G.G.Prive, A.Melnick. A Small-Molecule Inhibitor of BCL6 Kills Dlbcl Cells in Vitro and in Vivo. Cancer Cell V. 17 400 2010.
ISSN: ISSN 1535-6108
PubMed: 20385364
DOI: 10.1016/J.CCR.2009.12.050