Chlorine in PDB 6ew7: Crystal Structure of the BCL6 Btb Domain in Complex with Anilinopyrimidine Ligand

The structure of Crystal Structure of the BCL6 Btb Domain in Complex with Anilinopyrimidine Ligand, PDB code: 6ew7 was solved by G.Robb, A.Ferguson, D.Hargreaves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.90 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	30.780, 39.290, 55.430, 83.98, 73.95, 67.11
R / Rfree (%)	20.7 / 23.6

The structure of Crystal Structure of the BCL6 Btb Domain in Complex with Anilinopyrimidine Ligand also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of the BCL6 Btb Domain in Complex with Anilinopyrimidine Ligand (pdb code 6ew7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of the BCL6 Btb Domain in Complex with Anilinopyrimidine Ligand, PDB code: 6ew7:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Crystal Structure of the BCL6 Btb Domain in Complex with Anilinopyrimidine Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the BCL6 Btb Domain in Complex with Anilinopyrimidine Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:21.4 occ:1.00 O A:HOH340 3.0 24.9 1.0 O A:HOH331 3.2 16.8 1.0 O B:HOH330 3.4 19.4 1.0 N A:HIS116 3.5 19.0 1.0 CB A:HIS116 3.5 20.5 1.0 N A:VAL117 3.6 16.0 1.0 CB A:MET114 3.7 11.8 1.0 C A:MET114 3.7 16.4 1.0 CG2 A:VAL117 3.7 17.4 1.0 CA A:MET114 3.8 10.8 1.0 CA A:HIS116 3.8 19.0 1.0 CD2 A:HIS116 3.9 26.8 1.0 O A:MET114 4.0 16.9 1.0 CG A:HIS116 4.1 24.5 1.0 C A:HIS116 4.1 21.2 1.0 N A:GLU115 4.1 15.3 1.0 CE2 A:PHE89 4.2 14.2 1.0 CB A:VAL117 4.4 17.4 1.0 C A:GLU115 4.5 20.7 1.0 O A:CYS53 4.5 14.7 1.0 CE A:MET114 4.5 13.4 1.0 CG A:MET114 4.5 12.5 1.0 CA A:VAL117 4.5 15.0 1.0 O B:HOH345 4.6 29.6 1.0 CZ A:PHE89 4.7 12.1 1.0 CA A:GLU115 4.9 16.5 1.0 O A:HOH345 4.9 28.6 1.0

Chlorine binding site 2 out of 6 in the Crystal Structure of the BCL6 Btb Domain in Complex with Anilinopyrimidine Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the BCL6 Btb Domain in Complex with Anilinopyrimidine Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:16.1 occ:1.00 CL1 A:C1W202 0.0 16.1 1.0 C7 A:C1W202 1.7 14.2 1.0 H4 A:C1W202 2.6 14.1 1.0 C8 A:C1W202 2.7 17.0 1.0 C6 A:C1W202 2.8 15.2 1.0 H5 A:C1W202 2.9 15.8 1.0 N A:C1W202 3.1 14.9 1.0 O A:MET51 3.3 10.7 1.0 C A:MET51 3.4 11.8 1.0 N A:ALA52 3.6 9.7 1.0 CA A:ALA52 3.6 8.7 1.0 CG B:LEU25 3.6 11.0 1.0 CD1 B:LEU25 3.7 12.2 1.0 CB B:ASN21 3.7 7.0 1.0 CD2 B:LEU25 3.7 12.4 1.0 CD1 A:TYR58 3.8 12.2 1.0 CB A:MET51 3.9 9.5 1.0 O B:ASN21 3.9 7.3 1.0 N1 A:C1W202 4.0 15.8 1.0 N2 A:C1W202 4.0 14.2 1.0 CG B:ASN21 4.2 18.8 1.0 CA A:MET51 4.3 7.2 1.0 CE1 A:TYR58 4.3 13.4 1.0 C B:ASN21 4.3 9.6 1.0 CB A:ALA52 4.4 9.1 1.0 C9 A:C1W202 4.4 17.0 1.0 C5 A:C1W202 4.4 13.3 1.0 CA B:ASN21 4.4 6.2 1.0 ND2 B:ASN21 4.4 13.1 1.0 C A:ALA52 4.7 14.1 1.0 OD1 B:ASN21 4.8 13.5 1.0 CG A:TYR58 4.9 10.3 1.0 H A:C1W202 5.0 11.4 1.0 O A:THR48 5.0 7.9 1.0

Chlorine binding site 3 out of 6 in the Crystal Structure of the BCL6 Btb Domain in Complex with Anilinopyrimidine Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the BCL6 Btb Domain in Complex with Anilinopyrimidine Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:41.4 occ:1.00 CL A:C1W202 0.0 41.4 1.0 C14 A:C1W202 1.7 36.4 1.0 C15 A:C1W202 2.7 30.8 1.0 H2 A:C1W202 2.7 17.8 1.0 H9 A:C1W202 2.7 30.2 1.0 C13 A:C1W202 2.7 36.2 1.0 O1 A:C1W202 2.9 42.6 1.0 C16 A:C1W202 3.1 41.0 1.0 H10 A:C1W202 3.4 42.8 1.0 C3 A:C1W202 3.4 17.4 1.0 H3 A:C1W202 3.6 18.4 1.0 O A:HOH368 3.7 36.1 1.0 C4 A:C1W202 3.9 18.5 1.0 C10 A:C1W202 4.0 26.8 1.0 C12 A:C1W202 4.0 32.3 1.0 O A:C1W202 4.2 39.7 1.0 C2 A:C1W202 4.4 18.2 1.0 C11 A:C1W202 4.5 29.9 1.0 O A:HOH312 4.6 30.3 1.0 CE2 A:TYR58 4.7 12.8 1.0 F A:C1W202 4.7 19.6 1.0 H8 A:C1W202 4.9 32.2 1.0 O A:HOH366 4.9 22.9 1.0 CD2 A:TYR58 4.9 11.3 1.0

Chlorine binding site 4 out of 6 in the Crystal Structure of the BCL6 Btb Domain in Complex with Anilinopyrimidine Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the BCL6 Btb Domain in Complex with Anilinopyrimidine Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:21.3 occ:1.00 O B:HOH354 3.3 15.8 1.0 O A:HOH352 3.4 21.4 1.0 CB B:HIS116 3.5 20.5 1.0 N B:HIS116 3.5 18.8 1.0 N B:VAL117 3.5 14.8 1.0 CB B:MET114 3.7 14.5 1.0 C B:MET114 3.7 17.8 1.0 CG2 B:VAL117 3.7 15.7 1.0 CA B:HIS116 3.8 18.8 1.0 CA B:MET114 3.8 13.2 1.0 O B:MET114 3.9 18.4 1.0 CD2 B:HIS116 3.9 27.2 1.0 CG B:HIS116 4.1 24.7 1.0 C B:HIS116 4.1 20.6 1.0 N B:GLU115 4.2 15.6 1.0 CE2 B:PHE89 4.2 13.4 1.0 CB B:VAL117 4.4 16.1 1.0 C B:GLU115 4.5 20.0 1.0 O B:CYS53 4.5 15.0 1.0 CG B:MET114 4.5 15.5 1.0 CA B:VAL117 4.5 13.8 1.0 CZ B:PHE89 4.6 11.1 1.0 CE B:MET114 4.6 14.1 1.0 CA B:GLU115 4.9 16.4 1.0

Chlorine binding site 5 out of 6 in the Crystal Structure of the BCL6 Btb Domain in Complex with Anilinopyrimidine Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of the BCL6 Btb Domain in Complex with Anilinopyrimidine Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:15.8 occ:1.00 CL1 B:C1W202 0.0 15.8 1.0 C7 B:C1W202 1.7 16.5 1.0 H4 B:C1W202 2.5 13.3 1.0 C8 B:C1W202 2.7 17.9 1.0 C6 B:C1W202 2.8 15.8 1.0 H5 B:C1W202 2.9 17.2 1.0 N B:C1W202 3.0 13.8 1.0 O B:MET51 3.3 10.6 1.0 C B:MET51 3.4 9.3 1.0 N B:ALA52 3.5 6.0 1.0 CA B:ALA52 3.6 6.5 1.0 CG A:LEU25 3.6 8.8 1.0 CB A:ASN21 3.7 7.4 1.0 CD1 A:LEU25 3.7 11.1 1.0 CD2 A:LEU25 3.7 12.4 1.0 CD1 B:TYR58 3.8 12.5 1.0 CB B:MET51 3.9 8.2 1.0 O A:ASN21 3.9 7.7 1.0 N1 B:C1W202 4.0 18.6 1.0 N2 B:C1W202 4.0 17.7 1.0 CG A:ASN21 4.2 17.9 1.0 CE1 B:TYR58 4.2 13.7 1.0 CA B:MET51 4.3 5.7 1.0 C A:ASN21 4.3 8.9 1.0 CB B:ALA52 4.4 7.5 1.0 CA A:ASN21 4.4 5.7 1.0 C9 B:C1W202 4.4 19.2 1.0 C5 B:C1W202 4.4 13.4 1.0 ND2 A:ASN21 4.4 14.8 1.0 C B:ALA52 4.7 11.0 1.0 OD1 A:ASN21 4.8 9.7 1.0 CG B:TYR58 4.9 10.5 1.0 H B:C1W202 4.9 14.0 1.0

Chlorine binding site 6 out of 6 in the Crystal Structure of the BCL6 Btb Domain in Complex with Anilinopyrimidine Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of the BCL6 Btb Domain in Complex with Anilinopyrimidine Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:48.4 occ:1.00 CL B:C1W202 0.0 48.4 1.0 C14 B:C1W202 1.7 43.1 1.0 C15 B:C1W202 2.7 35.5 1.0 C13 B:C1W202 2.7 43.8 1.0 H9 B:C1W202 2.7 35.3 1.0 O B:HOH372 3.1 29.4 1.0 C16 B:C1W202 3.1 49.8 1.0 H2 B:C1W202 3.2 17.1 1.0 O1 B:C1W202 3.5 53.4 1.0 O B:C1W202 3.8 48.9 1.0 H10 B:C1W202 3.8 53.5 1.0 C3 B:C1W202 3.8 17.0 1.0 C10 B:C1W202 4.0 31.4 1.0 H3 B:C1W202 4.0 15.3 1.0 C12 B:C1W202 4.0 39.2 1.0 C4 B:C1W202 4.2 14.6 1.0 O B:HOH370 4.4 20.3 1.0 C11 B:C1W202 4.5 34.9 1.0 C2 B:C1W202 4.7 18.3 1.0 H8 B:C1W202 4.9 39.1 1.0 F B:C1W202 5.0 22.9 1.0

W.Mccoull, T.Cheung, E.Anderson, P.Barton, J.Burgess, K.Byth, Q.Cao, M.P.Castaldi, H.Chen, E.Chiarparin, R.J.Carbajo, E.Code, S.Cowan, P.R.Davey, A.D.Ferguson, S.Fillery, N.O.Fuller, N.Gao, D.Hargreaves, M.R.Howard, J.Hu, A.Kawatkar, P.D.Kemmitt, E.Leo, D.M.Molina, N.O'connell, P.Petteruti, T.Rasmusson, P.Raubo, P.B.Rawlins, P.Ricchiuto, G.R.Robb, M.Schenone, M.J.Waring, M.Zinda, S.Fawell, D.M.Wilson. Development of A Novel B-Cell Lymphoma 6 (BCL6) Protac to Provide Insight Into Small Molecule Targeting of BCL6. Acs Chem. Biol. V. 13 3131 2018.
ISSN: ESSN 1554-8937
PubMed: 30335946
DOI: 10.1021/ACSCHEMBIO.8B00698