Fluorine in PDB 6v1b: Crystal Structure of the Bromodomain of Human BRD9 Bound to I-BRD9

The structure of Crystal Structure of the Bromodomain of Human BRD9 Bound to I-BRD9, PDB code: 6v1b was solved by M.R.Karim, A.Chan, E.Schonbrunn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.61 / 1.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.990, 38.500, 60.920, 90.00, 108.99, 90.00
R / Rfree (%)	18.3 / 20.3

The binding sites of Fluorine atom in the Crystal Structure of the Bromodomain of Human BRD9 Bound to I-BRD9 (pdb code 6v1b). 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 Bromodomain of Human BRD9 Bound to I-BRD9, PDB code: 6v1b:
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 Bromodomain of Human BRD9 Bound to I-BRD9


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 Bromodomain of Human BRD9 Bound to I-BRD9 within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:33.3 occ:1.00 F23 A:H1B302 0.0 33.3 1.0 C22 A:H1B302 1.4 23.2 1.0 F25 A:H1B302 2.2 23.0 1.0 F24 A:H1B302 2.3 29.5 1.0 C19 A:H1B302 2.4 16.1 1.0 H20 A:H1B302 2.6 18.2 1.0 C20 A:H1B302 2.8 15.2 1.0 HH A:TYR222 2.8 30.9 1.0 OH A:TYR222 3.3 25.8 1.0 HD13 A:ILE169 3.6 57.6 1.0 C17 A:H1B302 3.7 17.5 1.0 O A:HOH454 3.8 33.3 1.0 H17 A:H1B302 4.0 21.0 1.0 O A:HOH480 4.0 32.3 1.0 HG13 A:ILE169 4.0 46.0 1.0 O A:HOH487 4.0 33.4 1.0 C12 A:H1B302 4.1 13.7 1.0 HG12 A:ILE169 4.2 46.0 1.0 HE1 A:PHE160 4.4 23.0 1.0 S27 A:H1B302 4.4 18.6 1.0 CG1 A:ILE169 4.4 38.3 1.0 CD1 A:ILE169 4.4 48.0 1.0 CZ A:TYR222 4.5 22.0 1.0 HE1 A:TYR222 4.7 27.6 1.0 C15 A:H1B302 4.8 17.7 1.0 HD1 A:PHE160 4.9 21.9 1.0 HD11 A:ILE169 4.9 57.6 1.0 C13 A:H1B302 5.0 20.5 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of the Bromodomain of Human BRD9 Bound to I-BRD9


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 Bromodomain of Human BRD9 Bound to I-BRD9 within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:29.5 occ:1.00 F24 A:H1B302 0.0 29.5 1.0 C22 A:H1B302 1.4 23.2 1.0 F25 A:H1B302 2.2 23.0 1.0 HE1 A:PHE160 2.3 23.0 1.0 F23 A:H1B302 2.3 33.3 1.0 C19 A:H1B302 2.4 16.1 1.0 H20 A:H1B302 3.0 18.2 1.0 HH A:TYR222 3.0 30.9 1.0 C20 A:H1B302 3.1 15.2 1.0 CE1 A:PHE160 3.1 19.2 1.0 HD1 A:PHE160 3.3 21.9 1.0 C17 A:H1B302 3.4 17.5 1.0 H17 A:H1B302 3.5 21.0 1.0 CD1 A:PHE160 3.6 18.2 1.0 O A:HOH487 3.7 33.4 1.0 OH A:TYR222 3.8 25.8 1.0 HE1 A:TYR222 4.1 27.6 1.0 CZ A:PHE160 4.2 20.3 1.0 C12 A:H1B302 4.3 13.7 1.0 HZ A:PHE160 4.4 24.3 1.0 C15 A:H1B302 4.6 17.7 1.0 CZ A:TYR222 4.8 22.0 1.0 CE1 A:TYR222 4.8 23.0 1.0 C13 A:H1B302 5.0 20.5 1.0 CG A:PHE160 5.0 17.1 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of the Bromodomain of Human BRD9 Bound to I-BRD9


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 Bromodomain of Human BRD9 Bound to I-BRD9 within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:23.0 occ:1.00 F25 A:H1B302 0.0 23.0 1.0 C22 A:H1B302 1.4 23.2 1.0 F24 A:H1B302 2.2 29.5 1.0 F23 A:H1B302 2.2 33.3 1.0 C19 A:H1B302 2.4 16.1 1.0 H17 A:H1B302 2.6 21.0 1.0 C17 A:H1B302 2.8 17.5 1.0 HD13 A:ILE169 3.4 57.6 1.0 C20 A:H1B302 3.6 15.2 1.0 H20 A:H1B302 3.9 18.2 1.0 C15 A:H1B302 4.2 17.7 1.0 CD1 A:ILE169 4.3 48.0 1.0 HG12 A:ILE169 4.4 46.0 1.0 HE1 A:PHE160 4.4 23.0 1.0 HD12 A:ILE169 4.5 57.6 1.0 HH A:TYR222 4.6 30.9 1.0 C12 A:H1B302 4.7 13.7 1.0 H15 A:H1B302 4.8 21.2 1.0 CG1 A:ILE169 4.8 38.3 1.0 HG13 A:ILE169 4.9 46.0 1.0 HD1 A:PHE160 4.9 21.9 1.0 C13 A:H1B302 5.0 20.5 1.0 HD11 A:ILE169 5.0 57.6 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of the Bromodomain of Human BRD9 Bound to I-BRD9


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 Bromodomain of Human BRD9 Bound to I-BRD9 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:39.5 occ:1.00 F23 B:H1B301 0.0 39.5 1.0 C22 B:H1B301 1.4 34.2 1.0 F24 B:H1B301 2.2 26.1 1.0 F25 B:H1B301 2.2 31.7 1.0 C19 B:H1B301 2.4 19.4 1.0 H20 B:H1B301 2.7 21.8 1.0 C20 B:H1B301 2.9 18.1 1.0 O B:HOH536 3.1 33.1 1.0 C17 B:H1B301 3.5 21.4 1.0 OH B:TYR222 3.5 24.9 1.0 O B:HOH410 3.7 29.7 1.0 HH B:TYR222 3.7 29.9 1.0 H17 B:H1B301 3.7 25.6 1.0 O B:HOH457 4.0 39.0 1.0 C12 B:H1B301 4.2 20.3 1.0 HD12 B:ILE169 4.4 44.8 1.0 S27 B:H1B301 4.4 19.1 1.0 HB B:ILE169 4.4 32.3 1.0 HE1 B:PHE160 4.5 27.4 1.0 O B:HOH475 4.5 26.1 1.0 C15 B:H1B301 4.6 23.0 1.0 CZ B:TYR222 4.7 20.6 1.0 C13 B:H1B301 4.9 18.3 1.0 HE1 B:TYR222 5.0 23.5 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of the Bromodomain of Human BRD9 Bound to I-BRD9


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 Bromodomain of Human BRD9 Bound to I-BRD9 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:26.1 occ:1.00 F24 B:H1B301 0.0 26.1 1.0 C22 B:H1B301 1.4 34.2 1.0 F23 B:H1B301 2.2 39.5 1.0 F25 B:H1B301 2.3 31.7 1.0 C19 B:H1B301 2.4 19.4 1.0 HE1 B:PHE160 2.4 27.4 1.0 H20 B:H1B301 3.0 21.8 1.0 C20 B:H1B301 3.0 18.1 1.0 CE1 B:PHE160 3.2 22.8 1.0 O B:HOH475 3.3 26.1 1.0 OH B:TYR222 3.3 24.9 1.0 C17 B:H1B301 3.4 21.4 1.0 H17 B:H1B301 3.6 25.6 1.0 HD1 B:PHE160 3.8 25.6 1.0 HH B:TYR222 3.8 29.9 1.0 HE1 B:TYR222 3.9 23.5 1.0 CD1 B:PHE160 3.9 21.3 1.0 HZ B:PHE160 4.1 28.6 1.0 CZ B:PHE160 4.1 23.8 1.0 O B:HOH536 4.2 33.1 1.0 C12 B:H1B301 4.3 20.3 1.0 CZ B:TYR222 4.4 20.6 1.0 CE1 B:TYR222 4.5 19.6 1.0 C15 B:H1B301 4.6 23.0 1.0 O B:HOH410 4.7 29.7 1.0 C13 B:H1B301 5.0 18.3 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of the Bromodomain of Human BRD9 Bound to I-BRD9


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 Bromodomain of Human BRD9 Bound to I-BRD9 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:31.7 occ:1.00 F25 B:H1B301 0.0 31.7 1.0 C22 B:H1B301 1.4 34.2 1.0 F23 B:H1B301 2.2 39.5 1.0 F24 B:H1B301 2.3 26.1 1.0 C19 B:H1B301 2.3 19.4 1.0 H17 B:H1B301 2.3 25.6 1.0 C17 B:H1B301 2.7 21.4 1.0 C20 B:H1B301 3.6 18.1 1.0 H20 B:H1B301 3.9 21.8 1.0 C15 B:H1B301 4.1 23.0 1.0 HE1 B:PHE160 4.1 27.4 1.0 H15 B:H1B301 4.6 27.6 1.0 O B:HOH536 4.7 33.1 1.0 C12 B:H1B301 4.7 20.3 1.0 O B:HOH476 4.8 29.9 1.0 HD1 B:PHE160 4.9 25.6 1.0 C13 B:H1B301 4.9 18.3 1.0 CE1 B:PHE160 4.9 22.8 1.0 HD12 B:ILE169 5.0 44.8 1.0

R.M.Karim, A.Chan, J.Y.Zhu, E.Schonbrunn. Structural Basis of Inhibitor Selectivity in the BRD7/9 Subfamily of Bromodomains. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32091206
DOI: 10.1021/ACS.JMEDCHEM.9B01980