Fluorine in PDB 5vbp: Crystal Structure of the First Bromodomain of Human BRD4 in Complex with RO3280

The structure of Crystal Structure of the First Bromodomain of Human BRD4 in Complex with RO3280, PDB code: 5vbp was solved by S.W.Ember, J.-Y.Zhu, E.Schonbrunn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.85 / 1.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.125, 59.452, 115.244, 90.00, 90.00, 90.00
R / Rfree (%)	14.3 / 20.7

The binding sites of Fluorine atom in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with RO3280 (pdb code 5vbp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with RO3280, PDB code: 5vbp:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with RO3280


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 of Human BRD4 in Complex with RO3280 within 5.0Å range: probe atom residue distance (Å) B Occ A:F204 b:9.4 occ:1.00 F19 A:79C204 0.0 9.4 1.0 C18 A:79C204 1.4 9.6 1.0 F20 A:79C204 2.2 11.9 1.0 C21 A:79C204 2.3 10.7 1.0 C16 A:79C204 2.4 10.2 1.0 H8 A:79C204 2.4 12.8 1.0 HG12 A:VAL87 2.5 12.9 1.0 C13 A:79C204 2.8 8.6 1.0 N14 A:79C204 2.9 9.5 1.0 C28 A:79C204 2.9 8.5 1.0 N22 A:79C204 3.0 10.4 1.0 HD11 A:LEU94 3.1 19.0 1.0 H7 A:79C204 3.2 12.8 1.0 HD13 A:LEU94 3.2 19.0 1.0 HD12 A:LEU94 3.2 19.0 1.0 HG22 A:VAL87 3.3 11.2 1.0 CD1 A:LEU94 3.3 15.8 1.0 HD11 A:LEU92 3.4 22.9 1.0 O17 A:79C204 3.4 11.4 1.0 HG21 A:VAL87 3.4 11.2 1.0 CG1 A:VAL87 3.5 10.8 1.0 HD13 A:LEU92 3.6 22.9 1.0 C12 A:79C204 3.8 9.7 1.0 CG2 A:VAL87 3.8 9.3 1.0 H21 A:79C204 3.8 14.7 1.0 N29 A:79C204 3.8 6.9 1.0 HG11 A:VAL87 3.9 12.9 1.0 CD1 A:LEU92 3.9 19.1 1.0 HE1 A:TYR97 3.9 11.1 1.0 HG13 A:VAL87 4.0 12.9 1.0 HD1 A:TYR97 4.1 10.8 1.0 CE1 A:TYR97 4.1 9.3 1.0 C23 A:79C204 4.2 12.0 1.0 HD12 A:LEU92 4.2 22.9 1.0 H17 A:79C204 4.2 11.6 1.0 CD1 A:TYR97 4.2 9.0 1.0 C15 A:79C204 4.3 10.1 1.0 CB A:VAL87 4.3 8.6 1.0 C27 A:79C204 4.4 12.3 1.0 N11 A:79C204 4.5 9.7 1.0 H4 A:79C204 4.5 12.2 1.0 C10 A:79C204 4.5 8.3 1.0 H22 A:79C204 4.6 14.7 1.0 HD22 A:ASN140 4.6 9.7 1.0 HG23 A:VAL87 4.7 11.2 1.0 H5 A:79C204 4.7 12.2 1.0 H18 A:79C204 4.8 14.4 1.0 H6 A:79C204 4.9 12.2 1.0 CG A:LEU94 4.9 16.6 1.0 H10 A:79C204 4.9 12.5 1.0 HD2 A:TYR139 4.9 12.7 1.0 CZ A:TYR97 4.9 10.4 1.0 HE2 A:TYR139 4.9 15.5 1.0 HA A:VAL87 4.9 10.6 1.0 HB A:VAL87 4.9 10.3 1.0 HG12 A:ILE146 5.0 10.2 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with RO3280


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 of Human BRD4 in Complex with RO3280 within 5.0Å range: probe atom residue distance (Å) B Occ A:F204 b:11.9 occ:1.00 F20 A:79C204 0.0 11.9 1.0 C18 A:79C204 1.3 9.6 1.0 F19 A:79C204 2.2 9.4 1.0 C16 A:79C204 2.3 10.2 1.0 C21 A:79C204 2.3 10.7 1.0 H7 A:79C204 2.4 12.8 1.0 H8 A:79C204 2.5 12.8 1.0 O17 A:79C204 2.6 11.4 1.0 HD2 A:TYR139 2.7 12.7 1.0 HD22 A:ASN140 2.9 9.7 1.0 HE1 A:TYR97 2.9 11.1 1.0 CD2 A:TYR139 3.1 10.6 1.0 HD1 A:TYR97 3.1 10.8 1.0 HD13 A:LEU94 3.3 19.0 1.0 HE2 A:TYR139 3.3 15.5 1.0 CE2 A:TYR139 3.4 12.9 1.0 CE1 A:TYR97 3.5 9.3 1.0 N14 A:79C204 3.6 9.5 1.0 CD1 A:TYR97 3.6 9.0 1.0 ND2 A:ASN140 3.6 8.1 1.0 N22 A:79C204 3.7 10.4 1.0 OD1 A:ASN140 3.7 9.2 1.0 HD11 A:LEU94 3.9 19.0 1.0 HB3 A:TYR139 3.9 11.9 1.0 CD1 A:LEU94 3.9 15.8 1.0 CG A:TYR139 4.0 10.4 1.0 HG12 A:VAL87 4.1 12.9 1.0 CG A:ASN140 4.1 8.2 1.0 C13 A:79C204 4.2 8.6 1.0 HD12 A:LEU94 4.2 19.0 1.0 C28 A:79C204 4.2 8.5 1.0 HD21 A:ASN140 4.3 9.7 1.0 HG21 A:VAL87 4.4 11.2 1.0 O A:HOH310 4.4 8.4 1.0 H10 A:79C204 4.5 12.5 1.0 CB A:TYR139 4.5 9.9 1.0 CZ A:TYR139 4.5 13.6 1.0 H21 A:79C204 4.5 14.7 1.0 CZ A:TYR97 4.6 10.4 1.0 HH A:TYR97 4.7 13.5 1.0 H4 A:79C204 4.7 12.2 1.0 C23 A:79C204 4.7 12.0 1.0 C15 A:79C204 4.7 10.1 1.0 HG12 A:ILE146 4.7 10.2 1.0 CG A:TYR97 4.8 9.4 1.0 HG21 A:ILE146 4.8 12.5 1.0 HB2 A:TYR139 4.9 11.9 1.0 HG22 A:VAL87 4.9 11.2 1.0 CD1 A:TYR139 4.9 12.3 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with RO3280


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 First Bromodomain of Human BRD4 in Complex with RO3280 within 5.0Å range: probe atom residue distance (Å) B Occ B:F204 b:12.9 occ:1.00 F19 B:79C204 0.0 12.9 1.0 C18 B:79C204 1.4 11.4 1.0 F20 B:79C204 2.2 12.2 1.0 C16 B:79C204 2.3 10.3 1.0 C21 B:79C204 2.3 9.8 1.0 H7 B:79C204 2.6 11.8 1.0 HG13 B:VAL87 2.7 11.1 1.0 C13 B:79C204 2.8 10.0 1.0 N14 B:79C204 2.8 10.3 1.0 HG11 B:VAL87 2.9 11.1 1.0 C28 B:79C204 3.0 9.3 1.0 N22 B:79C204 3.0 10.0 1.0 HD11 B:LEU92 3.0 17.8 1.0 HG23 B:VAL87 3.1 11.3 1.0 HD12 B:LEU94 3.1 23.6 1.0 H8 B:79C204 3.2 11.8 1.0 CG1 B:VAL87 3.3 9.2 1.0 O17 B:79C204 3.3 8.9 1.0 HD13 B:LEU92 3.4 17.8 1.0 HD11 B:LEU94 3.4 23.6 1.0 HD13 B:LEU94 3.4 23.6 1.0 CD1 B:LEU94 3.5 19.7 1.0 CD1 B:LEU92 3.6 14.9 1.0 C12 B:79C204 3.7 8.8 1.0 HD12 B:LEU92 3.8 17.8 1.0 N29 B:79C204 3.9 10.0 1.0 CG2 B:VAL87 4.0 9.4 1.0 H21 B:79C204 4.0 12.2 1.0 HG12 B:VAL87 4.0 11.1 1.0 HE1 B:TYR97 4.1 12.1 1.0 H17 B:79C204 4.2 10.5 1.0 C23 B:79C204 4.2 9.9 1.0 C15 B:79C204 4.2 7.4 1.0 CB B:VAL87 4.2 9.0 1.0 HD1 B:TYR97 4.2 12.8 1.0 CE1 B:TYR97 4.4 10.1 1.0 CD1 B:TYR97 4.4 10.7 1.0 H5 B:79C204 4.4 8.9 1.0 HG21 B:VAL87 4.4 11.3 1.0 C27 B:79C204 4.4 10.2 1.0 N11 B:79C204 4.5 11.1 1.0 HG22 B:VAL87 4.6 11.3 1.0 C10 B:79C204 4.6 10.7 1.0 H22 B:79C204 4.6 12.2 1.0 H6 B:79C204 4.6 8.9 1.0 HD22 B:ASN140 4.7 11.2 1.0 HE2 B:TYR139 4.7 15.7 1.0 H4 B:79C204 4.8 8.9 1.0 H10 B:79C204 4.8 10.6 1.0 H18 B:79C204 4.8 11.8 1.0 HA B:VAL87 4.8 11.8 1.0 HD2 B:TYR139 4.9 14.6 1.0 HB B:VAL87 4.9 10.8 1.0 HB3 B:LEU92 4.9 18.1 1.0 CG B:LEU92 4.9 15.8 1.0 HB2 B:LEU92 5.0 18.1 1.0 CG B:LEU94 5.0 17.9 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with RO3280


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 First Bromodomain of Human BRD4 in Complex with RO3280 within 5.0Å range: probe atom residue distance (Å) B Occ B:F204 b:12.2 occ:1.00 F20 B:79C204 0.0 12.2 1.0 C18 B:79C204 1.4 11.4 1.0 F19 B:79C204 2.2 12.9 1.0 C16 B:79C204 2.3 10.3 1.0 C21 B:79C204 2.4 9.8 1.0 H7 B:79C204 2.5 11.8 1.0 H8 B:79C204 2.5 11.8 1.0 O17 B:79C204 2.6 8.9 1.0 HD2 B:TYR139 2.7 14.6 1.0 HD22 B:ASN140 3.0 11.2 1.0 HE1 B:TYR97 3.0 12.1 1.0 HE2 B:TYR139 3.0 15.7 1.0 CD2 B:TYR139 3.1 12.2 1.0 HD1 B:TYR97 3.1 12.8 1.0 HD13 B:LEU94 3.2 23.6 1.0 CE2 B:TYR139 3.3 13.0 1.0 OD1 B:ASN140 3.4 11.1 1.0 CE1 B:TYR97 3.5 10.1 1.0 CD1 B:TYR97 3.6 10.7 1.0 N14 B:79C204 3.6 10.3 1.0 ND2 B:ASN140 3.7 9.4 1.0 N22 B:79C204 3.7 10.0 1.0 HD11 B:LEU94 3.9 23.6 1.0 CD1 B:LEU94 3.9 19.7 1.0 HD12 B:LEU94 3.9 23.6 1.0 CG B:ASN140 3.9 11.1 1.0 HG11 B:VAL87 4.0 11.1 1.0 CG B:TYR139 4.1 10.9 1.0 HG23 B:VAL87 4.1 11.3 1.0 HB3 B:TYR139 4.2 12.3 1.0 C13 B:79C204 4.2 10.0 1.0 C28 B:79C204 4.3 9.3 1.0 CZ B:TYR139 4.4 12.2 1.0 HD21 B:ASN140 4.4 11.2 1.0 H10 B:79C204 4.4 10.6 1.0 HG13 B:VAL87 4.5 11.1 1.0 O B:HOH309 4.5 7.3 1.0 H21 B:79C204 4.6 12.2 1.0 CZ B:TYR97 4.7 9.3 1.0 CG1 B:VAL87 4.7 9.2 1.0 CB B:TYR139 4.7 10.3 1.0 H5 B:79C204 4.7 8.9 1.0 HG12 B:ILE146 4.8 10.2 1.0 C15 B:79C204 4.8 7.4 1.0 C23 B:79C204 4.8 9.9 1.0 CG B:TYR97 4.8 10.4 1.0 O B:HOH403 4.9 22.3 1.0 HD11 B:LEU92 5.0 17.8 1.0

S.W.Ember, N.Berndt, J.-Y.Zhu, R.M.Karim, E.Schonbrunn. Dual Brd-PLK1 Inhibitors To Be Published.