Fluorine in PDB 3omk: Crystal Structure of Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide

The structure of Crystal Structure of Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide, PDB code: 3omk was solved by M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.68 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.320, 84.710, 190.010, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.5

The structure of Crystal Structure of Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide (pdb code 3omk). 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 Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide, PDB code: 3omk:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide


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 Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:32.6 occ:1.00 F20 A:OMK1 0.0 32.6 1.0 C11 A:OMK1 1.4 27.1 1.0 C13 A:OMK1 2.4 25.2 1.0 C8 A:OMK1 2.4 26.8 1.0 F21 A:OMK1 2.6 29.4 1.0 CG2 A:ILE339 3.3 31.1 1.0 CD1 A:ILE277 3.5 36.5 1.0 CG2 A:THR274 3.6 35.5 1.0 C4 A:OMK1 3.6 22.4 1.0 C10 A:OMK1 3.7 22.9 1.0 CG2 A:ILE273 3.8 43.4 1.0 C5 A:OMK1 4.1 21.2 1.0 CD1 A:LEU352 4.2 37.8 1.0 CB A:ILE339 4.3 29.0 1.0 CD2 A:LEU352 4.5 36.3 1.0 CB A:ILE273 4.5 44.5 1.0 N A:THR274 4.7 33.3 1.0 CB A:THR274 4.7 37.5 1.0 CD1 A:ILE356 4.7 30.2 1.0 CA A:THR274 4.7 33.2 1.0 CG A:LEU352 4.8 39.1 1.0 C A:ILE273 4.8 39.6 1.0 N1 A:OMK1 4.9 24.6 1.0 CD1 A:ILE339 4.9 34.9 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide


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 Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:29.4 occ:1.00 F21 A:OMK1 0.0 29.4 1.0 C13 A:OMK1 1.3 25.2 1.0 C11 A:OMK1 2.3 27.1 1.0 C10 A:OMK1 2.4 22.9 1.0 F20 A:OMK1 2.6 32.6 1.0 CA A:PHE340 3.1 26.9 1.0 N A:PHE340 3.2 26.7 1.0 CB A:PHE340 3.3 28.4 1.0 CD1 A:PHE340 3.6 34.8 1.0 CD2 A:LEU352 3.6 36.3 1.0 C8 A:OMK1 3.6 26.8 1.0 C5 A:OMK1 3.7 21.2 1.0 O A:SER336 3.7 26.8 1.0 CG2 A:ILE339 3.8 31.1 1.0 C A:ILE339 3.8 30.6 1.0 CG A:PHE340 3.9 30.2 1.0 CD1 A:ILE356 4.0 30.2 1.0 C4 A:OMK1 4.1 22.4 1.0 CB A:ILE339 4.1 29.0 1.0 O A:ILE339 4.3 30.7 1.0 CG A:LEU352 4.4 39.1 1.0 C A:PHE340 4.5 32.5 1.0 CA A:ILE339 4.6 25.6 1.0 CG2 A:THR274 4.6 35.5 1.0 CD1 A:LEU352 4.6 37.8 1.0 CE1 A:PHE340 4.8 36.2 1.0 C A:SER336 4.8 26.0 1.0 N3 A:OMK1 4.9 23.1 1.0 O A:PHE340 4.9 32.7 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide


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 Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide within 5.0Å range: probe atom residue distance (Å) B Occ C:F2 b:34.2 occ:1.00 F20 C:OMK2 0.0 34.2 1.0 C11 C:OMK2 1.3 30.7 1.0 C13 C:OMK2 2.4 27.6 1.0 C8 C:OMK2 2.4 28.9 1.0 F21 C:OMK2 2.7 36.1 1.0 CG2 C:ILE339 3.3 36.1 1.0 CG2 C:THR274 3.5 47.5 1.0 C4 C:OMK2 3.6 22.8 1.0 C10 C:OMK2 3.7 24.5 1.0 CD1 C:ILE277 3.7 43.2 1.0 CG2 C:ILE273 3.9 52.6 1.0 C5 C:OMK2 4.1 21.4 1.0 CD2 C:LEU352 4.2 44.5 1.0 CD1 C:ILE273 4.2 63.4 1.0 CD1 C:LEU352 4.2 42.0 1.0 CD1 C:ILE356 4.4 36.7 1.0 CB C:ILE339 4.5 32.7 1.0 CG C:LEU352 4.6 42.2 1.0 CG1 C:ILE273 4.7 54.2 1.0 CB C:THR274 4.7 50.1 1.0 N C:THR274 4.7 45.5 1.0 CA C:THR274 4.7 45.1 1.0 CB C:ILE273 4.9 53.8 1.0 C C:ILE273 4.9 50.5 1.0 N1 C:OMK2 4.9 26.4 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide


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 Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide within 5.0Å range: probe atom residue distance (Å) B Occ C:F2 b:36.1 occ:1.00 F21 C:OMK2 0.0 36.1 1.0 C13 C:OMK2 1.4 27.6 1.0 C11 C:OMK2 2.4 30.7 1.0 C10 C:OMK2 2.4 24.5 1.0 F20 C:OMK2 2.7 34.2 1.0 CA C:PHE340 3.3 34.8 1.0 CB C:PHE340 3.3 38.1 1.0 N C:PHE340 3.3 32.9 1.0 CD2 C:LEU352 3.5 44.5 1.0 C5 C:OMK2 3.6 21.4 1.0 C8 C:OMK2 3.7 28.9 1.0 CD1 C:PHE340 3.7 47.7 1.0 O C:SER336 3.8 30.9 1.0 CG2 C:ILE339 3.8 36.1 1.0 C C:ILE339 4.0 36.2 1.0 CG C:PHE340 4.0 42.7 1.0 CD1 C:ILE356 4.0 36.7 1.0 C4 C:OMK2 4.1 22.8 1.0 CG C:LEU352 4.3 42.2 1.0 CB C:ILE339 4.4 32.7 1.0 O C:ILE339 4.5 36.2 1.0 CG2 C:THR274 4.6 47.5 1.0 C C:PHE340 4.8 40.4 1.0 CA C:ILE339 4.8 29.0 1.0 CD1 C:LEU352 4.8 42.0 1.0 C C:SER336 4.9 30.5 1.0 N3 C:OMK2 4.9 26.2 1.0 CE1 C:PHE340 5.0 49.8 1.0

H.G.F.Richter, G.M.Benson, K.H.Bleicher, D.Blum, E.Chaput, N.Clemann, S.Feng, C.Gardes, U.Grether, P.Hartman, B.Kuhn, R.E.Martin, J.M.Plancher, M.G.Rudolph, F.Schuler, S.Taylor. Optimization of A Novel Class of Benzimidazole-Based Farnesoid X Receptor (Fxr) Agonists to Improve Physicochemical and Adme Properties Bioorg.Med.Chem.Lett. V. 21 1134 2011.
ISSN: ISSN 0960-894X
PubMed: 21269824
DOI: 10.1016/J.BMCL.2010.12.123