Fluorine in PDB 7lwg: Crystal Structure of the BCL6 Btb Domain in Complex with Oicr-12694

The structure of Crystal Structure of the BCL6 Btb Domain in Complex with Oicr-12694, PDB code: 7lwg was solved by D.A.Kuntz, G.G.Prive, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.11 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	31.786, 72.939, 55.336, 90, 106.32, 90
R / Rfree (%)	14.4 / 18.4

The structure of Crystal Structure of the BCL6 Btb Domain in Complex with Oicr-12694 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of the BCL6 Btb Domain in Complex with Oicr-12694 (pdb code 7lwg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the BCL6 Btb Domain in Complex with Oicr-12694, PDB code: 7lwg:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of the BCL6 Btb Domain in Complex with Oicr-12694


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 the BCL6 Btb Domain in Complex with Oicr-12694 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:10.0 occ:1.00 F08 A:YN7201 0.0 10.0 1.0 C07 A:YN7201 1.4 8.6 1.0 H181 A:YN7201 2.3 10.4 1.0 C09 A:YN7201 2.3 9.3 1.0 C06 A:YN7201 2.4 7.1 1.0 F10 A:YN7201 2.6 10.4 1.0 C18 A:YN7201 2.7 8.7 1.0 HD22 B:ASN21 2.8 12.9 1.0 C05 A:YN7201 2.8 7.5 1.0 O A:ALA52 2.9 8.2 1.0 HD21 B:ASN21 3.0 12.9 1.0 ND2 B:ASN21 3.2 10.8 1.0 HB3 B:ASP17 3.3 14.3 1.0 HA A:CYS53 3.3 8.0 1.0 O B:HOH356 3.5 28.2 1.0 C11 A:YN7201 3.6 8.8 1.0 C17 A:YN7201 3.6 7.4 1.0 O B:HOH375 3.7 29.2 1.0 N19 A:YN7201 3.9 8.4 1.0 C A:ALA52 4.1 6.6 1.0 C13 A:YN7201 4.1 8.3 1.0 C04 A:YN7201 4.1 7.8 1.0 CB B:ASP17 4.1 11.9 1.0 CA A:CYS53 4.2 6.7 1.0 HB2 B:ASP17 4.2 14.3 1.0 HA B:VAL18 4.4 9.3 1.0 H171 A:YN7201 4.4 8.9 1.0 CG B:ASN21 4.5 10.7 1.0 O B:ASP17 4.5 8.5 1.0 HG22 B:VAL18 4.5 11.6 1.0 C B:ASP17 4.6 8.4 1.0 H202 A:YN7201 4.6 11.1 1.0 N A:CYS53 4.6 6.1 1.0 C40 A:YN7201 4.6 7.5 1.0 O A:HOH327 4.6 12.6 1.0 C A:CYS53 4.6 8.2 1.0 H121 A:YN7201 4.6 12.3 1.0 O12 A:YN7201 4.7 10.2 1.0 O A:CYS53 4.7 8.8 1.0 N B:VAL18 4.8 8.1 1.0 C20 A:YN7201 4.8 9.2 1.0 HG23 B:VAL18 4.8 11.6 1.0 HB2 B:ASN21 4.8 10.7 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of the BCL6 Btb Domain in Complex with Oicr-12694


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 the BCL6 Btb Domain in Complex with Oicr-12694 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:10.4 occ:1.00 F10 A:YN7201 0.0 10.4 1.0 C09 A:YN7201 1.4 9.3 1.0 C07 A:YN7201 2.3 8.6 1.0 H121 A:YN7201 2.4 12.3 1.0 C11 A:YN7201 2.4 8.8 1.0 HB2 B:ASP17 2.5 14.3 1.0 F08 A:YN7201 2.6 10.0 1.0 O12 A:YN7201 2.7 10.2 1.0 HD1 B:HIS14 2.7 8.6 1.0 HB3 B:ASP17 2.8 14.3 1.0 CB B:ASP17 3.1 11.9 1.0 ND1 B:HIS14 3.2 7.1 1.0 HA B:HIS14 3.2 9.9 1.0 HG23 B:VAL18 3.4 11.6 1.0 O B:HOH317 3.5 16.5 1.0 O B:HIS14 3.6 8.1 1.0 C13 A:YN7201 3.7 8.3 1.0 C06 A:YN7201 3.7 7.1 1.0 HE1 B:HIS14 3.7 8.7 1.0 CE1 B:HIS14 3.7 7.2 1.0 H B:VAL18 3.8 9.7 1.0 OD2 B:ASP17 3.9 19.1 1.0 HG22 B:VAL18 3.9 11.6 1.0 N B:VAL18 4.0 8.1 1.0 CG B:ASP17 4.0 17.0 1.0 CA B:HIS14 4.0 8.2 1.0 CG2 B:VAL18 4.1 9.7 1.0 CG B:HIS14 4.1 6.8 1.0 C17 A:YN7201 4.1 7.4 1.0 O B:HOH375 4.1 29.2 1.0 C B:ASP17 4.2 8.4 1.0 CA B:ASP17 4.2 8.8 1.0 O A:HOH327 4.2 12.6 1.0 C B:HIS14 4.3 8.7 1.0 HA A:CYS53 4.4 8.0 1.0 HA B:VAL18 4.5 9.3 1.0 CB B:HIS14 4.5 6.5 1.0 H162 A:YN7201 4.6 13.1 1.0 H B:ASP17 4.6 10.2 1.0 H181 A:YN7201 4.7 10.4 1.0 HB2 B:HIS14 4.7 7.9 1.0 O A:ALA52 4.7 8.2 1.0 HG21 B:VAL18 4.7 11.6 1.0 NE2 B:HIS14 4.7 7.4 1.0 CA B:VAL18 4.8 7.7 1.0 C05 A:YN7201 4.8 7.5 1.0 O B:ASP17 4.8 8.5 1.0 N B:ASP17 4.9 8.5 1.0 HA B:ASP17 5.0 10.5 1.0 CD2 B:HIS14 5.0 6.8 1.0 C14 A:YN7201 5.0 8.7 1.0 HD22 B:ASN21 5.0 12.9 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of the BCL6 Btb Domain in Complex with Oicr-12694


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 the BCL6 Btb Domain in Complex with Oicr-12694 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:11.8 occ:1.00 F36 A:YN7201 0.0 11.8 1.0 C35 A:YN7201 1.3 8.5 1.0 N34 A:YN7201 2.3 9.7 1.0 C37 A:YN7201 2.3 8.6 1.0 HB3 B:ARG24 2.6 12.6 0.6 HD23 B:LEU25 2.8 13.8 1.0 HB3 B:ARG24 2.8 10.3 0.5 HB2 B:ARG24 2.9 12.6 0.6 HB2 B:ARG24 2.9 10.3 0.5 CL38 A:YN7201 3.0 13.3 1.0 HE1 A:TYR58 3.1 19.8 1.0 CB B:ARG24 3.2 10.5 0.6 CB B:ARG24 3.3 8.6 0.5 HD2 B:ARG28 3.3 22.2 1.0 HG B:LEU25 3.3 11.6 1.0 HD21 B:LEU25 3.4 13.8 1.0 CD2 B:LEU25 3.5 11.5 1.0 C25 A:YN7201 3.5 9.9 1.0 C23 A:YN7201 3.6 8.7 1.0 HD3 B:ARG24 3.6 16.4 0.6 N B:LEU25 3.6 7.6 1.0 H B:LEU25 3.6 9.1 0.6 HA B:LEU25 3.7 9.4 1.0 H B:LEU25 3.7 9.1 0.5 C B:ARG24 3.7 8.3 0.5 CE1 A:TYR58 3.7 16.5 1.0 C B:ARG24 3.8 7.8 0.6 CG B:LEU25 3.9 9.7 1.0 O B:ASN21 4.0 7.9 1.0 O B:ARG24 4.0 9.7 0.5 HD2 B:ARG24 4.0 12.4 0.5 C24 A:YN7201 4.1 8.9 1.0 CA B:LEU25 4.1 7.9 1.0 CA B:ARG24 4.1 7.8 0.5 CA B:ARG24 4.1 8.2 0.6 HE B:ARG24 4.2 14.2 0.5 HD12 B:ILE30 4.2 18.6 1.0 CD B:ARG24 4.2 13.7 0.6 CD B:ARG28 4.3 18.5 1.0 O B:ARG24 4.3 9.5 0.6 HD22 B:LEU25 4.3 13.8 1.0 CG B:ARG24 4.3 12.8 0.6 HD2 B:ARG24 4.4 16.4 0.6 H331 A:YN7201 4.4 21.9 1.0 HD1 A:TYR58 4.4 14.2 1.0 NE B:ARG24 4.4 11.8 0.5 OH A:TYR58 4.4 21.5 1.0 HE B:ARG28 4.4 23.5 1.0 CZ A:TYR58 4.4 17.8 1.0 CD1 A:TYR58 4.4 11.8 1.0 CG B:ARG24 4.5 9.8 0.5 CD B:ARG24 4.5 10.4 0.5 HD3 B:ARG28 4.6 22.2 1.0 CB B:LEU25 4.6 8.2 1.0 HA B:ASN21 4.6 9.7 1.0 N26 A:YN7201 4.6 12.8 1.0 NE B:ARG28 4.7 19.6 1.0 HA B:ARG24 4.7 9.8 0.6 H332 A:YN7201 4.7 21.9 1.0 HA B:ARG24 4.8 9.4 0.5 N22 A:YN7201 4.8 8.0 1.0 HG2 B:ARG24 4.8 15.3 0.6 HB3 B:ASN21 4.8 10.7 1.0 C33 A:YN7201 4.8 18.2 1.0 HG3 B:ARG24 4.9 11.8 0.5 CZ B:ARG24 4.9 11.9 0.5 HB2 B:ARG28 4.9 18.8 1.0 C B:ASN21 5.0 7.1 1.0 H221 A:YN7201 5.0 9.6 1.0 H241 A:YN7201 5.0 10.7 1.0 HG3 B:ARG24 5.0 15.3 0.6 H B:ARG24 5.0 9.3 0.5

Fluorine binding site 4 out of 6 in the Crystal Structure of the BCL6 Btb Domain in Complex with Oicr-12694


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 the BCL6 Btb Domain in Complex with Oicr-12694 within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:10.2 occ:1.00 F08 B:YN7201 0.0 10.2 1.0 C07 B:YN7201 1.4 9.1 1.0 C09 B:YN7201 2.3 8.6 1.0 H181 B:YN7201 2.3 10.2 1.0 C06 B:YN7201 2.4 7.8 1.0 F10 B:YN7201 2.6 10.3 1.0 C18 B:YN7201 2.7 8.5 1.0 C05 B:YN7201 2.8 8.0 1.0 O B:ALA52 3.0 7.5 1.0 HD22 A:ASN21 3.1 10.4 1.0 HB3 A:ASP17 3.2 14.0 1.0 HD21 A:ASN21 3.3 10.4 1.0 HA B:CYS53 3.4 7.6 1.0 ND2 A:ASN21 3.5 8.7 1.0 C11 B:YN7201 3.6 8.2 1.0 O A:HOH365 3.6 28.5 1.0 C17 B:YN7201 3.7 8.7 1.0 O3 B:GOL202 3.7 17.1 0.8 HO3 B:GOL202 3.8 20.6 0.8 N19 B:YN7201 4.0 7.5 1.0 H31 B:GOL202 4.0 21.6 0.8 C13 B:YN7201 4.1 8.1 1.0 CB A:ASP17 4.1 11.6 1.0 H2 B:GOL202 4.1 20.7 0.8 C04 B:YN7201 4.2 8.7 1.0 HB2 A:ASP17 4.2 14.0 1.0 C B:ALA52 4.2 6.5 1.0 CA B:CYS53 4.3 6.3 1.0 C3 B:GOL202 4.3 18.0 0.8 H171 B:YN7201 4.4 10.4 1.0 O B:HOH335 4.6 10.7 1.0 HA A:VAL18 4.6 8.7 1.0 HG22 A:VAL18 4.6 12.5 1.0 C40 B:YN7201 4.7 7.8 1.0 O12 B:YN7201 4.7 9.2 1.0 C A:ASP17 4.7 8.4 1.0 O A:ASP17 4.7 8.7 1.0 N B:CYS53 4.7 6.6 1.0 C B:CYS53 4.7 6.8 1.0 H202 B:YN7201 4.8 9.9 1.0 CG A:ASN21 4.8 6.3 1.0 C2 B:GOL202 4.8 17.2 0.8 HG23 A:VAL18 4.8 12.5 1.0 H121 B:YN7201 4.8 11.0 1.0 C20 B:YN7201 4.8 8.2 1.0 O B:CYS53 4.8 7.9 1.0 N A:VAL18 4.9 7.6 1.0 HD1 A:HIS14 4.9 8.5 1.0 OD2 A:ASP17 4.9 16.3 1.0 O39 B:YN7201 4.9 10.7 1.0 CG A:ASP17 5.0 15.3 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of the BCL6 Btb Domain in Complex with Oicr-12694


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the BCL6 Btb Domain in Complex with Oicr-12694 within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:10.3 occ:1.00 F10 B:YN7201 0.0 10.3 1.0 C09 B:YN7201 1.4 8.6 1.0 C07 B:YN7201 2.3 9.1 1.0 C11 B:YN7201 2.4 8.2 1.0 HB2 A:ASP17 2.6 14.0 1.0 F08 B:YN7201 2.6 10.2 1.0 HD1 A:HIS14 2.6 8.5 1.0 O12 B:YN7201 2.7 9.2 1.0 H121 B:YN7201 2.7 11.0 1.0 HB3 A:ASP17 2.8 14.0 1.0 HA A:HIS14 3.1 8.9 1.0 CB A:ASP17 3.1 11.6 1.0 ND1 A:HIS14 3.1 7.1 1.0 HO3 B:GOL202 3.4 20.6 0.8 HG23 A:VAL18 3.5 12.5 1.0 O B:HOH324 3.5 13.5 1.0 C13 B:YN7201 3.6 8.1 1.0 O A:HIS14 3.7 7.5 1.0 C06 B:YN7201 3.7 7.8 1.0 CE1 A:HIS14 3.7 7.4 1.0 HE1 A:HIS14 3.7 8.9 1.0 H31 B:GOL202 3.7 21.6 0.8 OD2 A:ASP17 3.7 16.3 1.0 O3 B:GOL202 3.9 17.1 0.8 CA A:HIS14 4.0 7.5 1.0 CG A:ASP17 4.0 15.3 1.0 H A:VAL18 4.0 9.1 1.0 CG A:HIS14 4.0 8.0 1.0 HG22 A:VAL18 4.1 12.5 1.0 C17 B:YN7201 4.2 8.7 1.0 N A:VAL18 4.2 7.6 1.0 O B:HOH335 4.2 10.7 1.0 CG2 A:VAL18 4.3 10.4 1.0 C A:HIS14 4.3 6.9 1.0 CA A:ASP17 4.3 9.8 1.0 C A:ASP17 4.3 8.4 1.0 C3 B:GOL202 4.4 18.0 0.8 CB A:HIS14 4.4 7.3 1.0 HA B:CYS53 4.5 7.6 1.0 H162 B:YN7201 4.5 12.2 1.0 HB2 A:HIS14 4.6 8.8 1.0 H181 B:YN7201 4.7 10.2 1.0 H A:ASP17 4.7 9.6 1.0 HA A:VAL18 4.7 8.7 1.0 NE2 A:HIS14 4.7 7.5 1.0 C05 B:YN7201 4.8 8.0 1.0 O B:ALA52 4.8 7.5 1.0 HG21 A:VAL18 4.9 12.5 1.0 CD2 A:HIS14 4.9 6.7 1.0 O A:ARG13 4.9 10.4 0.6 CA A:VAL18 4.9 7.3 1.0 C14 B:YN7201 4.9 9.7 1.0 O A:ARG13 5.0 10.9 0.4 N A:ASP17 5.0 8.0 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of the BCL6 Btb Domain in Complex with Oicr-12694


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the BCL6 Btb Domain in Complex with Oicr-12694 within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:10.1 occ:1.00 F36 B:YN7201 0.0 10.1 1.0 C35 B:YN7201 1.3 8.6 1.0 N34 B:YN7201 2.3 9.5 1.0 C37 B:YN7201 2.3 8.1 1.0 HB2 A:ARG24 2.8 11.1 1.0 HD23 A:LEU25 2.8 12.4 1.0 HB3 A:ARG24 2.9 11.1 1.0 CL38 B:YN7201 2.9 9.1 1.0 HG A:LEU25 3.0 10.8 1.0 HH11 A:ARG28 3.1 26.0 1.0 HE1 B:TYR58 3.1 11.2 1.0 HD21 A:LEU25 3.2 12.4 1.0 CB A:ARG24 3.3 9.2 1.0 CD2 A:LEU25 3.3 10.3 1.0 C25 B:YN7201 3.5 9.8 1.0 NH1 A:ARG28 3.5 21.7 1.0 C23 B:YN7201 3.6 8.4 1.0 HH12 A:ARG28 3.6 26.0 1.0 CG A:LEU25 3.6 9.0 1.0 H A:LEU25 3.6 8.4 1.0 O A:ASN21 3.6 7.3 1.0 N A:LEU25 3.7 7.0 1.0 HD3 A:ARG24 3.7 14.0 1.0 HD3 A:ARG28 3.8 27.6 1.0 HA A:LEU25 3.9 8.2 1.0 CE1 B:TYR58 3.9 9.4 1.0 C A:ARG24 3.9 7.8 1.0 C24 B:YN7201 4.1 9.3 1.0 HA A:ASN21 4.2 7.9 1.0 CA A:LEU25 4.2 6.8 1.0 H331 B:YN7201 4.2 14.8 1.0 CA A:ARG24 4.2 7.8 1.0 HD22 A:LEU25 4.3 12.4 1.0 HB3 A:ASN21 4.3 8.8 1.0 CD A:ARG24 4.3 11.7 1.0 HD2 A:ARG24 4.3 14.0 1.0 CG A:ARG24 4.4 9.2 1.0 HD1 B:TYR58 4.4 10.0 1.0 CZ A:ARG28 4.4 23.8 1.0 CB A:LEU25 4.5 7.2 1.0 O A:ARG24 4.5 9.5 1.0 CD A:ARG28 4.5 23.0 1.0 HD2 A:ARG28 4.6 27.6 1.0 CD1 B:TYR58 4.6 8.3 1.0 C A:ASN21 4.6 6.2 1.0 OH B:TYR58 4.6 13.6 1.0 CZ B:TYR58 4.6 12.2 1.0 N26 B:YN7201 4.7 11.9 1.0 HD11 A:LEU25 4.7 12.4 1.0 CA A:ASN21 4.7 6.6 1.0 N22 B:YN7201 4.7 7.4 1.0 CD1 A:LEU25 4.8 10.3 1.0 HD12 A:ILE30 4.8 17.3 1.0 H221 B:YN7201 4.8 8.8 1.0 NE A:ARG28 4.9 23.9 1.0 OD1 A:ASN21 4.9 8.8 1.0 C33 B:YN7201 4.9 12.3 1.0 CB A:ASN21 4.9 7.3 1.0 HG2 A:ARG24 4.9 11.1 1.0 HA A:ARG24 4.9 9.3 1.0 HE2 B:MET51 4.9 13.3 1.0 HB2 A:LEU25 5.0 8.6 1.0 H A:ARG24 5.0 8.5 1.0 H241 B:YN7201 5.0 11.1 1.0

A.Mamai, M.Isaac. Discovery of OICR12694: A Novel, Potent, Selective and Orally Bioavailable BCL6 Btb Inhibitor To Be Published.