Fluorine in PDB 5dy7: Crystal Structure of the Human BRPF1 Bromodomain in Complex with SEED4

The structure of Crystal Structure of the Human BRPF1 Bromodomain in Complex with SEED4, PDB code: 5dy7 was solved by J.Zhu, A.Caflisch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.19 / 1.69
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	60.667, 60.667, 62.382, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 20.4

The binding sites of Fluorine atom in the Crystal Structure of the Human BRPF1 Bromodomain in Complex with SEED4 (pdb code 5dy7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the Human BRPF1 Bromodomain in Complex with SEED4, PDB code: 5dy7:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of the Human BRPF1 Bromodomain in Complex with SEED4


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 Human BRPF1 Bromodomain in Complex with SEED4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:58.0 occ:1.00 FAB A:5GT801 0.0 58.0 1.0 CAO A:5GT801 1.3 52.0 1.0 FAD A:5GT801 2.1 53.2 1.0 FAC A:5GT801 2.1 53.3 1.0 CAL A:5GT801 2.2 43.2 1.0 CAE A:5GT801 2.6 38.1 1.0 OE1 A:GLU661 2.7 79.7 1.0 CD A:GLU661 3.2 77.1 1.0 CG A:PRO658 3.3 43.9 1.0 CAG A:5GT801 3.5 40.0 1.0 OE2 A:GLU661 3.6 81.2 1.0 CB A:GLU661 3.8 54.3 1.0 CD A:PRO658 3.9 40.4 1.0 CAF A:5GT801 4.0 33.5 1.0 CG A:GLU661 4.1 67.1 1.0 CAN A:5GT801 4.6 35.6 1.0 CB A:PRO658 4.6 46.5 1.0 CAM A:5GT801 4.8 33.2 1.0 CG2 A:VAL662 4.9 40.3 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of the Human BRPF1 Bromodomain in Complex with SEED4


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 Human BRPF1 Bromodomain in Complex with SEED4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:53.3 occ:1.00 FAC A:5GT801 0.0 53.3 1.0 CAO A:5GT801 1.3 52.0 1.0 FAD A:5GT801 2.1 53.2 1.0 FAB A:5GT801 2.1 58.0 1.0 CAL A:5GT801 2.2 43.2 1.0 CAE A:5GT801 3.0 38.1 1.0 CAG A:5GT801 3.1 40.0 1.0 OE1 A:GLU661 3.8 79.7 1.0 CZ A:PHE714 3.9 37.1 1.0 CAF A:5GT801 4.3 33.5 1.0 CE2 A:PHE714 4.3 38.1 1.0 CAN A:5GT801 4.3 35.6 1.0 CAM A:5GT801 4.8 33.2 1.0 CD A:GLU661 4.8 77.1 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of the Human BRPF1 Bromodomain in Complex with SEED4


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 Human BRPF1 Bromodomain in Complex with SEED4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:53.2 occ:1.00 FAD A:5GT801 0.0 53.2 1.0 CAO A:5GT801 1.3 52.0 1.0 FAB A:5GT801 2.1 58.0 1.0 FAC A:5GT801 2.1 53.3 1.0 CAL A:5GT801 2.2 43.2 1.0 CAG A:5GT801 2.6 40.0 1.0 CG2 A:VAL662 3.2 40.3 1.0 CAE A:5GT801 3.5 38.1 1.0 CB A:GLU661 3.6 54.3 1.0 OE1 A:GLU661 3.8 79.7 1.0 CAN A:5GT801 4.0 35.6 1.0 CG A:PRO658 4.3 43.9 1.0 CD A:GLU661 4.3 77.1 1.0 O A:HOH1027 4.4 38.4 1.0 O A:GLU661 4.4 48.6 1.0 C A:GLU661 4.4 51.5 1.0 CG A:GLU661 4.6 67.1 1.0 CD A:PRO658 4.6 40.4 1.0 CAF A:5GT801 4.6 33.5 1.0 CA A:GLU661 4.6 52.3 1.0 CB A:VAL662 4.7 44.0 1.0 N A:VAL662 4.8 55.4 1.0 CAM A:5GT801 4.8 33.2 1.0 NAJ A:5GT801 4.9 31.3 1.0

J.Zhu, A.Caflisch. Twenty Crystal Structures of Bromodomain and Phd Finger Containing Protein 1 (BRPF1)/Ligand Complexes Reveal Conserved Binding Motifs and Rare Interactions. J.Med.Chem. V. 59 5555 2016.
ISSN: ISSN 0022-2623
PubMed: 27167503
DOI: 10.1021/ACS.JMEDCHEM.6B00215