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Fluorine in PDB 7mr5: Crystal Structure of the First Bromodomain (BD1) of Human BRD4 Bound to Gxh-II-052

Protein crystallography data

The structure of Crystal Structure of the First Bromodomain (BD1) of Human BRD4 Bound to Gxh-II-052, PDB code: 7mr5 was solved by A.Chan, E.Schonbrunn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.37 / 1.82
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 30.08, 39.71, 57.18, 99.95, 104.45, 89.99
R / Rfree (%) 15.9 / 21.2

Other elements in 7mr5:

The structure of Crystal Structure of the First Bromodomain (BD1) of Human BRD4 Bound to Gxh-II-052 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the First Bromodomain (BD1) of Human BRD4 Bound to Gxh-II-052 (pdb code 7mr5). 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 Bound to Gxh-II-052, PDB code: 7mr5:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7mr5

Go back to Fluorine Binding Sites List in 7mr5
Fluorine binding site 1 out of 2 in the Crystal Structure of the First Bromodomain (BD1) of Human BRD4 Bound to Gxh-II-052


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 Bound to Gxh-II-052 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:25.4
occ:1.00
F72 A:ZMS201 0.0 25.4 1.0
C71 A:ZMS201 1.4 20.5 1.0
C70 A:ZMS201 2.4 12.7 1.0
C42 A:ZMS201 2.4 18.7 1.0
N39 A:ZMS201 2.7 22.5 1.0
C40 A:ZMS201 3.0 25.4 1.0
CH2 A:TRP81 3.3 26.9 1.0
CZ3 A:TRP81 3.4 22.2 1.0
CD1 B:LEU94 3.6 27.2 1.0
C45 A:ZMS201 3.6 15.5 1.0
C43 A:ZMS201 3.7 21.3 1.0
CG B:LEU94 3.9 28.5 1.0
CD1 B:LEU92 3.9 20.2 1.0
CD2 B:LEU94 4.0 24.5 1.0
C36 A:ZMS201 4.0 26.3 1.0
O41 A:ZMS201 4.1 35.7 1.0
C44 A:ZMS201 4.1 18.9 1.0
CB B:LEU92 4.2 18.0 1.0
CZ2 A:TRP81 4.3 21.3 1.0
CE3 A:TRP81 4.4 20.2 1.0
C37 A:ZMS201 4.4 23.8 1.0
C53 A:ZMS201 4.5 20.0 1.0
CG B:LEU92 4.5 19.2 1.0
C52 A:ZMS201 4.7 14.6 1.0
O A:GLN78 4.8 15.7 1.0
CD2 B:LEU92 4.8 23.7 1.0
O A:HOH330 4.9 25.6 1.0
N46 A:ZMS201 4.9 11.0 1.0
N48 A:ZMS201 5.0 8.4 1.0
C54 A:ZMS201 5.0 11.6 1.0

Fluorine binding site 2 out of 2 in 7mr5

Go back to Fluorine Binding Sites List in 7mr5
Fluorine binding site 2 out of 2 in the Crystal Structure of the First Bromodomain (BD1) of Human BRD4 Bound to Gxh-II-052


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 Bound to Gxh-II-052 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:27.6
occ:1.00
F74 A:ZMS201 0.0 27.6 1.0
C73 A:ZMS201 1.4 27.2 1.0
C75 A:ZMS201 2.4 19.4 1.0
C10 A:ZMS201 2.4 27.2 1.0
C11 A:ZMS201 3.0 42.0 1.0
N13 A:ZMS201 3.1 44.2 1.0
N82 A:ZMS201 3.2 16.3 1.0
CD2 A:LEU92 3.5 34.5 1.0
C07 A:ZMS201 3.6 16.7 1.0
O84 A:ZMS201 3.7 23.0 1.0
C09 A:ZMS201 3.7 28.3 1.0
O A:HOH342 3.7 29.4 1.0
C81 A:ZMS201 3.7 19.7 1.0
O12 A:ZMS201 3.9 43.9 1.0
S83 A:ZMS201 3.9 22.4 1.0
C80 A:ZMS201 4.0 14.6 1.0
C08 A:ZMS201 4.2 22.5 1.0
O85 A:ZMS201 4.2 21.0 1.0
CB A:LEU92 4.3 29.1 1.0
CG A:LEU92 4.3 29.0 1.0
C14 A:ZMS201 4.4 52.1 1.0
C19 A:ZMS201 4.5 53.0 1.0
CD1 A:LEU92 4.5 26.8 1.0
CD2 A:LEU94 4.6 38.0 1.0
C90 A:ZMS201 4.6 23.6 1.0
O A:LEU92 4.7 44.8 1.0
N76 A:ZMS201 4.8 10.1 1.0
N06 A:ZMS201 4.9 13.1 1.0
CD1 A:LEU94 4.9 28.8 1.0

Reference:

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
Page generated: Tue Jul 15 21:50:24 2025

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