Fluorine in PDB 6v17: Crystal Structure of the Bromodomain of Human BRD7 Bound to I-BRD9

The structure of Crystal Structure of the Bromodomain of Human BRD7 Bound to I-BRD9, PDB code: 6v17 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)	38.59 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.102, 64.749, 96.107, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 24.1

The structure of Crystal Structure of the Bromodomain of Human BRD7 Bound to I-BRD9 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of the Bromodomain of Human BRD7 Bound to I-BRD9 (pdb code 6v17). 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 BRD7 Bound to I-BRD9, PDB code: 6v17:
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 BRD7 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 BRD7 Bound to I-BRD9 within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:66.9 occ:1.00 F23 A:H1B302 0.0 66.9 1.0 C22 A:H1B302 1.4 66.8 1.0 F24 A:H1B302 2.2 72.8 1.0 F25 A:H1B302 2.2 72.8 1.0 C19 A:H1B302 2.4 54.2 1.0 C17 A:H1B302 3.2 45.9 1.0 C20 A:H1B302 3.2 46.6 1.0 CD1 A:ILE164 3.2 44.6 1.0 CG1 A:ILE164 3.5 50.1 1.0 OH A:TYR217 3.9 52.8 1.0 C12 A:H1B302 4.4 39.7 1.0 C15 A:H1B302 4.4 41.5 1.0 CZ A:TYR217 4.8 49.5 1.0 CE1 A:TYR217 4.9 44.2 1.0 C13 A:H1B302 4.9 41.0 1.0 S27 A:H1B302 5.0 35.9 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of the Bromodomain of Human BRD7 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 BRD7 Bound to I-BRD9 within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:72.8 occ:1.00 F24 A:H1B302 0.0 72.8 1.0 C22 A:H1B302 1.4 66.8 1.0 F25 A:H1B302 2.2 72.8 1.0 F23 A:H1B302 2.2 66.9 1.0 C19 A:H1B302 2.4 54.2 1.0 OH A:TYR217 2.7 52.8 1.0 C20 A:H1B302 2.7 46.6 1.0 CE1 A:TYR217 3.0 44.2 1.0 CZ A:TYR217 3.3 49.5 1.0 CE1 A:PHE155 3.6 43.9 1.0 C17 A:H1B302 3.6 45.9 1.0 C12 A:H1B302 4.1 39.7 1.0 CD1 A:PHE155 4.2 39.5 1.0 CD1 A:TYR217 4.2 35.1 1.0 CZ A:PHE155 4.4 42.5 1.0 CE2 A:TYR217 4.6 44.7 1.0 S27 A:H1B302 4.6 35.9 1.0 C15 A:H1B302 4.8 41.5 1.0 C13 A:H1B302 4.9 41.0 1.0 C11 A:H1B302 4.9 35.5 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of the Bromodomain of Human BRD7 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 BRD7 Bound to I-BRD9 within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:72.8 occ:1.00 F25 A:H1B302 0.0 72.8 1.0 C22 A:H1B302 1.4 66.8 1.0 F24 A:H1B302 2.2 72.8 1.0 F23 A:H1B302 2.2 66.9 1.0 C19 A:H1B302 2.3 54.2 1.0 C17 A:H1B302 2.8 45.9 1.0 C20 A:H1B302 3.5 46.6 1.0 CE1 A:PHE155 4.0 43.9 1.0 C15 A:H1B302 4.1 41.5 1.0 CD1 A:PHE155 4.5 39.5 1.0 C12 A:H1B302 4.7 39.7 1.0 OH A:TYR217 4.9 52.8 1.0 C13 A:H1B302 4.9 41.0 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of the Bromodomain of Human BRD7 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 BRD7 Bound to I-BRD9 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:59.9 occ:1.00 F23 B:H1B301 0.0 59.9 1.0 C22 B:H1B301 1.4 58.7 1.0 F25 B:H1B301 2.2 62.3 1.0 F24 B:H1B301 2.2 62.4 1.0 C19 B:H1B301 2.4 51.1 1.0 OH B:TYR217 2.7 60.4 1.0 C20 B:H1B301 2.8 47.2 1.0 CZ B:TYR217 3.6 54.4 1.0 C17 B:H1B301 3.6 43.4 1.0 CE1 B:TYR217 3.6 54.3 1.0 CD1 B:ILE164 3.8 52.8 1.0 CG1 B:ILE164 4.0 51.3 1.0 C12 B:H1B301 4.2 45.7 1.0 S27 B:H1B301 4.3 39.7 1.0 C15 B:H1B301 4.7 41.4 1.0 CE2 B:TYR217 4.8 49.4 1.0 CD1 B:TYR217 5.0 50.9 1.0 C13 B:H1B301 5.0 43.9 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of the Bromodomain of Human BRD7 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 BRD7 Bound to I-BRD9 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:62.4 occ:1.00 F24 B:H1B301 0.0 62.4 1.0 C22 B:H1B301 1.4 58.7 1.0 F25 B:H1B301 2.2 62.3 1.0 F23 B:H1B301 2.2 59.9 1.0 C19 B:H1B301 2.4 51.1 1.0 C20 B:H1B301 3.1 47.2 1.0 CE1 B:PHE155 3.2 58.6 1.0 C17 B:H1B301 3.3 43.4 1.0 CE1 B:TYR217 3.8 54.3 1.0 CD1 B:PHE155 3.9 55.2 1.0 OH B:TYR217 3.9 60.4 1.0 CZ B:PHE155 4.0 47.1 1.0 C12 B:H1B301 4.3 45.7 1.0 CZ B:TYR217 4.4 54.4 1.0 C15 B:H1B301 4.5 41.4 1.0 CD1 B:TYR217 4.8 50.9 1.0 C13 B:H1B301 4.9 43.9 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of the Bromodomain of Human BRD7 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 BRD7 Bound to I-BRD9 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:62.3 occ:1.00 F25 B:H1B301 0.0 62.3 1.0 C22 B:H1B301 1.4 58.7 1.0 F23 B:H1B301 2.2 59.9 1.0 F24 B:H1B301 2.2 62.4 1.0 C19 B:H1B301 2.4 51.1 1.0 C17 B:H1B301 2.8 43.4 1.0 C20 B:H1B301 3.6 47.2 1.0 CD1 B:ILE164 3.7 52.8 1.0 C15 B:H1B301 4.2 41.4 1.0 CG1 B:ILE164 4.5 51.3 1.0 C12 B:H1B301 4.8 45.7 1.0 OH B:TYR217 4.8 60.4 1.0 C13 B:H1B301 5.0 43.9 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