Fluorine in PDB 8ujy: Crystal Structure of Human Wd Repeat-Containing Protein 5 in Complex with 4-(3,5-Dimethoxybenzyl)-9-(4-Fluoro-2-Methylphenyl)-7-((2-Imino- 3-Methyl-2,3-Dihydro-1H-Imidazol-1-Yl)Methyl)-3,4-Dihydrobenzo[F][1, 4]Oxazepin-5(2H)-One (Compound 8)

The structure of Crystal Structure of Human Wd Repeat-Containing Protein 5 in Complex with 4-(3,5-Dimethoxybenzyl)-9-(4-Fluoro-2-Methylphenyl)-7-((2-Imino- 3-Methyl-2,3-Dihydro-1H-Imidazol-1-Yl)Methyl)-3,4-Dihydrobenzo[F][1, 4]Oxazepin-5(2H)-One (Compound 8), PDB code: 8ujy was solved by B.Zhao, K.Amporndanai, S.W.Fesik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.66 / 2.01
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.81, 47.68, 68.869, 88.04, 89.27, 74.66
R / Rfree (%)	18.8 / 23.2

The binding sites of Fluorine atom in the Crystal Structure of Human Wd Repeat-Containing Protein 5 in Complex with 4-(3,5-Dimethoxybenzyl)-9-(4-Fluoro-2-Methylphenyl)-7-((2-Imino- 3-Methyl-2,3-Dihydro-1H-Imidazol-1-Yl)Methyl)-3,4-Dihydrobenzo[F][1, 4]Oxazepin-5(2H)-One (Compound 8) (pdb code 8ujy). 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 Human Wd Repeat-Containing Protein 5 in Complex with 4-(3,5-Dimethoxybenzyl)-9-(4-Fluoro-2-Methylphenyl)-7-((2-Imino- 3-Methyl-2,3-Dihydro-1H-Imidazol-1-Yl)Methyl)-3,4-Dihydrobenzo[F][1, 4]Oxazepin-5(2H)-One (Compound 8), PDB code: 8ujy:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Human Wd Repeat-Containing Protein 5 in Complex with 4-(3,5-Dimethoxybenzyl)-9-(4-Fluoro-2-Methylphenyl)-7-((2-Imino- 3-Methyl-2,3-Dihydro-1H-Imidazol-1-Yl)Methyl)-3,4-Dihydrobenzo[F][1, 4]Oxazepin-5(2H)-One (Compound 8)


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 Human Wd Repeat-Containing Protein 5 in Complex with 4-(3,5-Dimethoxybenzyl)-9-(4-Fluoro-2-Methylphenyl)-7-((2-Imino- 3-Methyl-2,3-Dihydro-1H-Imidazol-1-Yl)Methyl)-3,4-Dihydrobenzo[F][1, 4]Oxazepin-5(2H)-One (Compound 8) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:32.3 occ:1.00 F1 A:VV3401 0.0 32.3 1.0 C22 A:VV3401 1.3 33.1 1.0 HA A:ALA65 2.2 10.6 1.0 C21 A:VV3401 2.3 34.9 1.0 C23 A:VV3401 2.3 36.1 1.0 H23 A:VV3401 2.5 34.0 1.0 H24 A:VV3401 2.5 34.8 1.0 HA3 A:GLY89 2.6 10.3 1.0 HB1 A:ALA65 2.8 11.3 1.0 CA A:ALA65 3.1 10.7 1.0 H A:ILE90 3.3 10.1 1.0 CB A:ALA65 3.3 11.2 1.0 CA A:GLY89 3.4 10.3 1.0 HB3 A:ALA65 3.5 11.1 1.0 N A:ILE90 3.5 10.2 1.0 C A:GLY89 3.5 9.9 1.0 C20 A:VV3401 3.6 33.4 1.0 O A:ILE90 3.6 8.7 1.0 O A:HOH740 3.6 41.0 1.0 C24 A:VV3401 3.6 37.0 1.0 N A:ALA65 3.6 9.4 1.0 HA2 A:GLY89 3.7 10.2 1.0 C A:ILE90 4.0 10.4 1.0 H A:ALA65 4.0 9.5 1.0 C19 A:VV3401 4.1 34.5 1.0 C A:SER64 4.2 8.7 1.0 HB2 A:ALA65 4.2 11.1 1.0 OD2 A:ASP107 4.2 19.5 1.0 O A:GLY89 4.2 8.8 1.0 O A:SER64 4.2 8.1 1.0 C A:ALA65 4.3 10.7 1.0 H22 A:VV3401 4.3 33.8 1.0 CA A:ILE90 4.4 10.1 1.0 HB3 A:SER49 4.4 11.5 1.0 O A:ALA65 4.4 9.9 1.0 HA A:SER91 4.5 11.1 1.0 N A:GLY89 4.5 10.3 1.0 H A:GLY89 4.6 10.7 1.0 N A:SER91 4.6 9.5 1.0 CG A:ASP107 4.8 18.2 1.0 O A:HOH745 4.8 28.4 1.0 HA A:ILE90 4.8 10.2 1.0 HG A:SER49 4.8 11.4 0.0 C25 A:VV3401 4.9 33.8 1.0 OD1 A:ASP107 4.9 17.9 1.0 O A:HOH650 4.9 13.9 1.0 OG A:SER91 4.9 16.1 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Human Wd Repeat-Containing Protein 5 in Complex with 4-(3,5-Dimethoxybenzyl)-9-(4-Fluoro-2-Methylphenyl)-7-((2-Imino- 3-Methyl-2,3-Dihydro-1H-Imidazol-1-Yl)Methyl)-3,4-Dihydrobenzo[F][1, 4]Oxazepin-5(2H)-One (Compound 8)


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 Human Wd Repeat-Containing Protein 5 in Complex with 4-(3,5-Dimethoxybenzyl)-9-(4-Fluoro-2-Methylphenyl)-7-((2-Imino- 3-Methyl-2,3-Dihydro-1H-Imidazol-1-Yl)Methyl)-3,4-Dihydrobenzo[F][1, 4]Oxazepin-5(2H)-One (Compound 8) within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:32.3 occ:1.00 F1 B:VV3401 0.0 32.3 1.0 C22 B:VV3401 1.4 33.4 1.0 HA B:ALA65 2.3 11.9 1.0 C21 B:VV3401 2.4 30.4 1.0 C23 B:VV3401 2.4 32.5 1.0 H23 B:VV3401 2.5 31.2 1.0 H24 B:VV3401 2.6 31.9 1.0 HA3 B:GLY89 2.6 8.9 1.0 HB1 B:ALA65 2.8 12.1 1.0 O B:HOH654 2.9 37.3 1.0 CA B:ALA65 3.1 12.1 1.0 H B:ILE90 3.3 9.3 1.0 CB B:ALA65 3.3 11.8 1.0 CA B:GLY89 3.4 8.9 1.0 N B:ILE90 3.5 9.0 1.0 O B:ILE90 3.5 12.6 1.0 C B:GLY89 3.6 8.9 1.0 N B:ALA65 3.6 10.8 1.0 C20 B:VV3401 3.6 31.3 1.0 C24 B:VV3401 3.6 31.5 1.0 HB3 B:ALA65 3.7 12.0 1.0 HA2 B:GLY89 3.7 8.9 1.0 C B:ILE90 3.9 11.2 1.0 H B:ALA65 3.9 11.3 1.0 C B:SER64 4.1 11.6 1.0 C19 B:VV3401 4.1 32.9 1.0 O B:SER64 4.2 11.3 1.0 HB2 B:ALA65 4.2 12.0 1.0 C B:ALA65 4.3 12.2 1.0 O B:GLY89 4.3 7.9 1.0 HB3 B:SER49 4.3 13.8 1.0 CA B:ILE90 4.3 10.3 1.0 H22 B:VV3401 4.4 31.4 1.0 OD2 B:ASP107 4.4 14.8 1.0 HA B:SER91 4.4 12.5 1.0 O B:ALA65 4.5 12.5 1.0 N B:SER91 4.6 11.3 1.0 N B:GLY89 4.6 8.8 1.0 H B:GLY89 4.7 9.3 1.0 HG B:SER49 4.7 9.2 0.0 O B:HOH695 4.8 30.6 1.0 HA B:ILE90 4.8 10.2 1.0 CG B:ASP107 4.8 14.4 1.0 C25 B:VV3401 4.9 29.7 1.0 O B:HOH546 5.0 30.9 1.0 OD1 B:ASP107 5.0 14.5 1.0 OG B:SER91 5.0 17.1 1.0

K.B.Teuscher, J.J.Mills, J.Tian, C.Han, K.M.Meyers, J.Sai, T.M.South, M.M.Crow, M.Van Meveren, J.L.Sensintaffar, B.Zhao, K.Amporndanai, W.J.Moore, G.M.Stott, W.P.Tansey, T.Lee, S.W.Fesik. Structure-Based Discovery of Potent, Orally Bioavailable Benzoxazepinone-Based Wd Repeat Domain 5 Inhibitors J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
DOI: 10.1021/ACS.JMEDCHEM.3C01529