Fluorine in PDB 5lj1: N-Terminal Bromodomain of Human BRD4 with 8-(((3R,4R,5S)-3-((4,4- Difluorocyclohexyl)Methoxy)-5-Methoxypiperidin-4-Yl)Amino)-3-Methyl- 5-(5-Methylpyridin-3-Yl)-1,7-Naphthyridin-2(1H)-One

The structure of N-Terminal Bromodomain of Human BRD4 with 8-(((3R,4R,5S)-3-((4,4- Difluorocyclohexyl)Methoxy)-5-Methoxypiperidin-4-Yl)Amino)-3-Methyl- 5-(5-Methylpyridin-3-Yl)-1,7-Naphthyridin-2(1H)-One, PDB code: 5lj1 was solved by C.Chung, P.Bamborough, E.Demont, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.67 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	41.670, 109.190, 30.260, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 23.7

The binding sites of Fluorine atom in the N-Terminal Bromodomain of Human BRD4 with 8-(((3R,4R,5S)-3-((4,4- Difluorocyclohexyl)Methoxy)-5-Methoxypiperidin-4-Yl)Amino)-3-Methyl- 5-(5-Methylpyridin-3-Yl)-1,7-Naphthyridin-2(1H)-One (pdb code 5lj1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the N-Terminal Bromodomain of Human BRD4 with 8-(((3R,4R,5S)-3-((4,4- Difluorocyclohexyl)Methoxy)-5-Methoxypiperidin-4-Yl)Amino)-3-Methyl- 5-(5-Methylpyridin-3-Yl)-1,7-Naphthyridin-2(1H)-One, PDB code: 5lj1:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the N-Terminal Bromodomain of Human BRD4 with 8-(((3R,4R,5S)-3-((4,4- Difluorocyclohexyl)Methoxy)-5-Methoxypiperidin-4-Yl)Amino)-3-Methyl- 5-(5-Methylpyridin-3-Yl)-1,7-Naphthyridin-2(1H)-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of N-Terminal Bromodomain of Human BRD4 with 8-(((3R,4R,5S)-3-((4,4- Difluorocyclohexyl)Methoxy)-5-Methoxypiperidin-4-Yl)Amino)-3-Methyl- 5-(5-Methylpyridin-3-Yl)-1,7-Naphthyridin-2(1H)-One within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:67.5 occ:1.00 F31 A:6XX202 0.0 67.5 1.0 C30 A:6XX202 1.4 62.1 1.0 F32 A:6XX202 2.2 62.5 1.0 C33 A:6XX202 2.4 58.1 1.0 C27 A:6XX202 2.4 57.3 1.0 O A:HOH404 2.5 50.8 1.0 O A:LEU92 2.9 52.7 1.0 C36 A:6XX202 3.7 49.5 1.0 C24 A:6XX202 3.7 50.0 1.0 O A:HOH333 4.0 58.4 1.0 C A:LEU92 4.0 50.5 1.0 C22 A:6XX202 4.1 45.7 1.0 CA A:LEU92 4.5 48.0 1.0 CB A:LEU92 4.9 44.7 1.0 CB A:ASN93 5.0 67.5 1.0

Fluorine binding site 2 out of 2 in the N-Terminal Bromodomain of Human BRD4 with 8-(((3R,4R,5S)-3-((4,4- Difluorocyclohexyl)Methoxy)-5-Methoxypiperidin-4-Yl)Amino)-3-Methyl- 5-(5-Methylpyridin-3-Yl)-1,7-Naphthyridin-2(1H)-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of N-Terminal Bromodomain of Human BRD4 with 8-(((3R,4R,5S)-3-((4,4- Difluorocyclohexyl)Methoxy)-5-Methoxypiperidin-4-Yl)Amino)-3-Methyl- 5-(5-Methylpyridin-3-Yl)-1,7-Naphthyridin-2(1H)-One within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:62.5 occ:1.00 F32 A:6XX202 0.0 62.5 1.0 C30 A:6XX202 1.4 62.1 1.0 F31 A:6XX202 2.2 67.5 1.0 C33 A:6XX202 2.4 58.1 1.0 C27 A:6XX202 2.4 57.3 1.0 C36 A:6XX202 3.0 49.5 1.0 C24 A:6XX202 3.1 50.0 1.0 C22 A:6XX202 3.6 45.7 1.0 O A:HOH333 3.8 58.4 1.0 O A:HOH404 4.0 50.8 1.0 O A:LEU92 4.7 52.7 1.0 C19 A:6XX202 4.8 37.7 1.0

P.Bamborough, C.W.Chung, E.H.Demont, R.C.Furze, A.J.Bannister, K.H.Che, H.Diallo, C.Douault, P.Grandi, T.Kouzarides, A.M.Michon, D.J.Mitchell, R.K.Prinjha, C.Rau, S.Robson, R.J.Sheppard, R.Upton, R.J.Watson. A Chemical Probe For the ATAD2 Bromodomain. Angew.Chem.Int.Ed.Engl. V. 55 11382 2016.
ISSN: ESSN 1521-3773
PubMed: 27530368
DOI: 10.1002/ANIE.201603928