Fluorine in PDB 7l9m: Crystal Structure of the First Bromodomain (BD1) of Human BRD4 in Complex with Bivalent Inhibitor Gxh-II-083

The structure of Crystal Structure of the First Bromodomain (BD1) of Human BRD4 in Complex with Bivalent Inhibitor Gxh-II-083, PDB code: 7l9m was solved by M.R.Karim, E.Schonbrunn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.08 / 1.45
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	30.27, 40.07, 57.35, 100.1, 104.61, 90.07
R / Rfree (%)	17.6 / 20.2

The structure of Crystal Structure of the First Bromodomain (BD1) of Human BRD4 in Complex with Bivalent Inhibitor Gxh-II-083 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of the First Bromodomain (BD1) of Human BRD4 in Complex with Bivalent Inhibitor Gxh-II-083 (pdb code 7l9m). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of the First Bromodomain (BD1) of Human BRD4 in Complex with Bivalent Inhibitor Gxh-II-083, PDB code: 7l9m:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of the First Bromodomain (BD1) of Human BRD4 in Complex with Bivalent Inhibitor Gxh-II-083


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 First Bromodomain (BD1) of Human BRD4 in Complex with Bivalent Inhibitor Gxh-II-083 within 5.0Å range: probe atom residue distance (Å) B Occ A:F204 b:20.3 occ:1.00 F80 A:XR4204 0.0 20.3 1.0 C79 A:XR4204 1.3 19.7 1.0 C78 A:XR4204 2.3 15.2 1.0 C50 A:XR4204 2.4 18.5 1.0 N47 A:XR4204 2.8 18.6 1.0 C48 A:XR4204 3.0 21.1 1.0 CH2 A:TRP81 3.3 24.2 1.0 CZ3 A:TRP81 3.3 18.5 1.0 C53 A:XR4204 3.5 14.5 1.0 C51 A:XR4204 3.6 18.1 1.0 CD1 B:LEU94 3.7 24.7 1.0 CG B:LEU94 3.9 27.6 1.0 CD1 B:LEU92 3.9 20.9 1.0 C52 A:XR4204 4.0 18.1 1.0 CD2 B:LEU94 4.1 21.3 1.0 C44 A:XR4204 4.2 20.2 1.0 O49 A:XR4204 4.2 24.3 1.0 CZ2 A:TRP81 4.4 21.5 1.0 C45 A:XR4204 4.4 24.0 1.0 CB B:LEU92 4.4 22.4 1.0 C61 A:XR4204 4.4 15.5 1.0 CE3 A:TRP81 4.4 17.7 1.0 CG B:LEU92 4.5 19.1 1.0 C60 A:XR4204 4.6 15.4 1.0 CD2 B:LEU92 4.6 23.1 1.0 N54 A:XR4204 4.8 12.9 1.0 O A:GLN78 4.9 17.4 1.0 N56 A:XR4204 4.9 13.4 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of the First Bromodomain (BD1) of Human BRD4 in Complex with Bivalent Inhibitor Gxh-II-083


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 First Bromodomain (BD1) of Human BRD4 in Complex with Bivalent Inhibitor Gxh-II-083 within 5.0Å range: probe atom residue distance (Å) B Occ A:F204 b:29.2 occ:1.00 F82 A:XR4204 0.0 29.2 1.0 C81 A:XR4204 1.3 28.6 1.0 C83 A:XR4204 2.3 21.3 1.0 C10 A:XR4204 2.4 31.0 1.0 C11 A:XR4204 2.9 41.2 1.0 N13 A:XR4204 3.2 42.0 1.0 N90 A:XR4204 3.3 17.6 1.0 O A:HOH391 3.6 31.1 1.0 C07 A:XR4204 3.6 20.2 1.0 C09 A:XR4204 3.6 28.1 1.0 O12 A:XR4204 3.6 45.3 1.0 CD2 A:LEU92 3.7 31.3 1.0 O92 A:XR4204 3.7 24.8 1.0 C89 A:XR4204 3.7 18.4 1.0 S91 A:XR4204 3.9 21.5 1.0 C88 A:XR4204 4.0 17.6 1.0 C08 A:XR4204 4.1 22.8 1.0 C15 A:XR4204 4.3 46.4 1.0 C16 A:XR4204 4.3 48.4 1.0 C14 A:XR4204 4.4 46.3 1.0 CB A:LEU92 4.4 31.4 1.0 O93 A:XR4204 4.4 20.5 1.0 CG A:LEU92 4.4 27.7 1.0 CD1 A:LEU92 4.5 25.5 1.0 C98 A:XR4204 4.6 20.4 1.0 O A:LEU92 4.7 40.6 1.0 N84 A:XR4204 4.8 15.3 1.0 N06 A:XR4204 4.8 17.2 1.0 CD1 A:LEU94 4.9 27.9 1.0

X.Guan, N.Cheryala, R.M.Karim, A.Chan, N.Berndt, J.Qi, G.I.Georg, E.Schonbrunn. Bivalent Bet Bromodomain Inhibitors Confer Increased Potency and Selectivity For Brdt Via Protein Conformational Plasticity. J.Med.Chem. V. 65 10441 2022.
ISSN: ISSN 0022-2623
PubMed: 35867655
DOI: 10.1021/ACS.JMEDCHEM.2C00453