Fluorine in PDB 7khl: BRD4-BD1 COMPOUND6 (Methyl 4-(3,5-Difluoropyridin-2-Yl)-10-Methyl-7- ((Methylsulfonyl)Methyl)-11-Oxo-3,4,10,11-Tetrahydro-1H-1,4,10- Triazadibenzo[Cd,F]Azulene-6-Carboxylate)

The structure of BRD4-BD1 COMPOUND6 (Methyl 4-(3,5-Difluoropyridin-2-Yl)-10-Methyl-7- ((Methylsulfonyl)Methyl)-11-Oxo-3,4,10,11-Tetrahydro-1H-1,4,10- Triazadibenzo[Cd,F]Azulene-6-Carboxylate), PDB code: 7khl was solved by J.M.Murray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.46 / 1.29
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	30.278, 41.812, 54.256, 84.58, 76.3, 89.92
R / Rfree (%)	19.3 / 22.5

The binding sites of Fluorine atom in the BRD4-BD1 COMPOUND6 (Methyl 4-(3,5-Difluoropyridin-2-Yl)-10-Methyl-7- ((Methylsulfonyl)Methyl)-11-Oxo-3,4,10,11-Tetrahydro-1H-1,4,10- Triazadibenzo[Cd,F]Azulene-6-Carboxylate) (pdb code 7khl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the BRD4-BD1 COMPOUND6 (Methyl 4-(3,5-Difluoropyridin-2-Yl)-10-Methyl-7- ((Methylsulfonyl)Methyl)-11-Oxo-3,4,10,11-Tetrahydro-1H-1,4,10- Triazadibenzo[Cd,F]Azulene-6-Carboxylate), PDB code: 7khl:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the BRD4-BD1 COMPOUND6 (Methyl 4-(3,5-Difluoropyridin-2-Yl)-10-Methyl-7- ((Methylsulfonyl)Methyl)-11-Oxo-3,4,10,11-Tetrahydro-1H-1,4,10- Triazadibenzo[Cd,F]Azulene-6-Carboxylate)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of BRD4-BD1 COMPOUND6 (Methyl 4-(3,5-Difluoropyridin-2-Yl)-10-Methyl-7- ((Methylsulfonyl)Methyl)-11-Oxo-3,4,10,11-Tetrahydro-1H-1,4,10- Triazadibenzo[Cd,F]Azulene-6-Carboxylate) within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:13.0 occ:0.65 F36 A:WEM201 0.0 13.0 0.7 C33 A:WEM201 1.3 12.3 0.7 C34 A:WEM201 2.3 12.6 0.7 C32 A:WEM201 2.4 11.7 0.7 N A:ILE146 3.2 12.5 1.0 CB A:ASP145 3.5 17.1 1.0 N35 A:WEM201 3.6 12.4 0.7 CA A:ILE146 3.6 11.6 1.0 O A:HOH419 3.6 16.6 1.0 SD A:MET149 3.6 17.2 1.0 C A:ASP145 3.6 13.6 1.0 C31 A:WEM201 3.6 11.2 0.7 CB A:ILE146 3.8 11.0 1.0 C30 A:WEM201 4.1 11.8 0.7 CA A:ASP145 4.2 14.8 1.0 O A:ASP145 4.2 14.3 1.0 CD1 A:ILE146 4.4 14.3 1.0 CG1 A:ILE146 4.7 12.2 1.0 O A:HOH315 4.7 21.6 1.0 F37 A:WEM201 4.7 12.5 0.7 CG A:ASP145 4.9 24.4 1.0 CG A:MET149 4.9 15.9 1.0 CE A:MET149 4.9 16.0 1.0 CG2 A:ILE146 4.9 11.4 1.0 N A:ASP145 4.9 15.3 1.0

Fluorine binding site 2 out of 2 in the BRD4-BD1 COMPOUND6 (Methyl 4-(3,5-Difluoropyridin-2-Yl)-10-Methyl-7- ((Methylsulfonyl)Methyl)-11-Oxo-3,4,10,11-Tetrahydro-1H-1,4,10- Triazadibenzo[Cd,F]Azulene-6-Carboxylate)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of BRD4-BD1 COMPOUND6 (Methyl 4-(3,5-Difluoropyridin-2-Yl)-10-Methyl-7- ((Methylsulfonyl)Methyl)-11-Oxo-3,4,10,11-Tetrahydro-1H-1,4,10- Triazadibenzo[Cd,F]Azulene-6-Carboxylate) within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:12.5 occ:0.65 F37 A:WEM201 0.0 12.5 0.7 C31 A:WEM201 1.4 11.2 0.7 C32 A:WEM201 2.3 11.7 0.7 C30 A:WEM201 2.4 11.8 0.7 C15 A:WEM201 2.6 11.5 0.7 C20 A:WEM201 2.9 12.8 0.7 CZ3 A:TRP81 2.9 17.1 1.0 N14 A:WEM201 2.9 11.4 0.7 CH2 A:TRP81 3.1 16.8 1.0 CB A:PRO82 3.1 11.8 1.0 C16 A:WEM201 3.2 11.3 0.7 CG A:PRO82 3.2 11.7 1.0 C19 A:WEM201 3.6 14.3 0.7 C33 A:WEM201 3.6 12.3 0.7 N35 A:WEM201 3.6 12.4 0.7 CE3 A:TRP81 3.7 15.7 1.0 C17 A:WEM201 3.8 12.5 0.7 C4 A:WEM201 3.9 11.2 0.7 C18 A:WEM201 3.9 13.7 0.7 CA A:PRO82 4.0 11.2 1.0 CZ2 A:TRP81 4.0 16.1 1.0 C34 A:WEM201 4.1 12.6 0.7 CD1 A:ILE146 4.2 14.3 1.0 C13 A:WEM201 4.3 11.1 0.7 CD A:PRO82 4.4 11.5 1.0 C21 A:WEM201 4.5 16.9 0.7 CD2 A:TRP81 4.5 14.9 1.0 C5 A:WEM201 4.5 10.9 0.7 N A:PRO82 4.6 11.7 1.0 C3 A:WEM201 4.6 10.8 0.7 CE2 A:TRP81 4.6 15.1 1.0 F36 A:WEM201 4.7 13.0 0.7 C6 A:WEM201 4.8 10.9 0.7 O22 A:WEM201 5.0 18.4 0.7

P.S.Dragovich, T.H.Pillow, R.A.Blake, J.D.Sadowsky, E.Adaligil, P.Adhikari, J.Chen, N.Corr, J.Dela Cruz-Chuh, G.Del Rosario, A.Fullerton, S.J.Hartman, F.Jiang, S.Kaufman, T.Kleinheinz, K.R.Kozak, L.Liu, Y.Lu, M.M.Mulvihill, J.M.Murray, A.O'donohue, R.K.Rowntree, W.S.Sawyer, L.R.Staben, J.Wai, J.Wang, B.Wei, W.Wei, Z.Xu, H.Yao, S.F.Yu, D.Zhang, H.Zhang, S.Zhang, Y.Zhao, H.Zhou, X.Zhu. Antibody-Mediated Delivery of Chimeric BRD4 Degraders. Part 2: Improvement of in Vitro Antiproliferation Activity and in Vivo Antitumor Efficacy. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 33596073
DOI: 10.1021/ACS.JMEDCHEM.0C01846