Fluorine in PDB 3olf: Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3-Methylbenzoic Acid

The structure of Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3-Methylbenzoic Acid, PDB code: 3olf 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)	28.44 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.280, 84.860, 191.560, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 23.8

The structure of Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3-Methylbenzoic Acid 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 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3-Methylbenzoic Acid (pdb code 3olf). 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 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3-Methylbenzoic Acid, PDB code: 3olf:
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 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3-Methylbenzoic Acid


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 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3-Methylbenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:30.1 occ:1.00 F26 A:OLF1 0.0 30.1 1.0 C11 A:OLF1 1.3 29.9 1.0 C15 A:OLF1 2.3 28.6 1.0 C8 A:OLF1 2.4 27.9 1.0 F27 A:OLF1 2.6 29.8 1.0 CG2 A:ILE339 3.3 34.8 1.0 CD1 A:ILE277 3.6 39.7 1.0 C4 A:OLF1 3.6 24.8 1.0 C10 A:OLF1 3.6 28.0 1.0 CG2 A:THR274 3.7 40.4 1.0 CG2 A:ILE273 4.0 51.9 1.0 C5 A:OLF1 4.1 23.6 1.0 CB A:ILE339 4.3 33.6 1.0 CD1 A:LEU352 4.3 36.9 1.0 CD2 A:LEU352 4.6 36.8 1.0 CD1 A:ILE356 4.7 29.4 1.0 CB A:ILE273 4.7 50.8 1.0 CB A:THR274 4.8 44.7 1.0 N A:THR274 4.8 38.7 1.0 CA A:THR274 4.9 37.8 1.0 N1 A:OLF1 4.9 26.9 1.0 CG A:LEU352 4.9 37.5 1.0 C A:ILE273 4.9 43.7 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3-Methylbenzoic Acid


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 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3-Methylbenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:29.8 occ:1.00 F27 A:OLF1 0.0 29.8 1.0 C15 A:OLF1 1.3 28.6 1.0 C11 A:OLF1 2.3 29.9 1.0 C10 A:OLF1 2.4 28.0 1.0 F26 A:OLF1 2.6 30.1 1.0 CA A:PHE340 3.1 30.4 1.0 N A:PHE340 3.1 29.4 1.0 CB A:PHE340 3.3 32.0 1.0 C8 A:OLF1 3.6 27.9 1.0 C5 A:OLF1 3.6 23.6 1.0 CD2 A:LEU352 3.6 36.8 1.0 O A:SER336 3.7 25.1 1.0 CD1 A:PHE340 3.7 37.0 1.0 C A:ILE339 3.8 34.0 1.0 CG2 A:ILE339 3.8 34.8 1.0 CD1 A:ILE356 4.0 29.4 1.0 CG A:PHE340 4.0 34.0 1.0 C4 A:OLF1 4.1 24.8 1.0 CB A:ILE339 4.2 33.6 1.0 O A:ILE339 4.3 35.2 1.0 CG A:LEU352 4.4 37.5 1.0 C A:PHE340 4.5 36.2 1.0 CA A:ILE339 4.6 29.9 1.0 CD1 A:LEU352 4.6 36.9 1.0 C A:SER336 4.7 26.4 1.0 N3 A:OLF1 4.9 23.6 1.0 CG2 A:THR274 4.9 40.4 1.0 CE1 A:PHE340 5.0 37.8 1.0 O A:PHE340 5.0 34.2 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3-Methylbenzoic Acid


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 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3-Methylbenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:F2 b:35.0 occ:1.00 F26 C:OLF2 0.0 35.0 1.0 C11 C:OLF2 1.3 30.9 1.0 C8 C:OLF2 2.3 29.8 1.0 C15 C:OLF2 2.4 32.0 1.0 F27 C:OLF2 2.7 33.8 1.0 CD1 C:ILE273 3.2 71.5 1.0 CG2 C:ILE339 3.3 40.1 1.0 C4 C:OLF2 3.6 29.1 1.0 C10 C:OLF2 3.6 30.5 1.0 CD1 C:ILE277 3.6 51.3 1.0 CG2 C:THR274 3.7 57.5 1.0 CG2 C:ILE273 3.9 56.1 1.0 CG1 C:ILE273 4.0 58.5 1.0 CD1 C:LEU352 4.1 45.3 1.0 C5 C:OLF2 4.1 29.9 1.0 CB C:ILE339 4.4 39.8 1.0 CD1 C:ILE356 4.4 42.8 1.0 CD2 C:LEU352 4.6 48.0 1.0 CB C:ILE273 4.6 57.6 1.0 CG C:LEU352 4.8 45.1 1.0 N1 C:OLF2 4.9 31.5 1.0 CB C:THR274 4.9 60.3 1.0 N C:THR274 4.9 52.5 1.0 CA C:THR274 4.9 52.4 1.0 CG1 C:ILE277 5.0 51.6 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3-Methylbenzoic Acid


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 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3-Methylbenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:F2 b:33.8 occ:1.00 F27 C:OLF2 0.0 33.8 1.0 C15 C:OLF2 1.4 32.0 1.0 C11 C:OLF2 2.4 30.9 1.0 C10 C:OLF2 2.4 30.5 1.0 F26 C:OLF2 2.7 35.0 1.0 CA C:PHE340 3.1 41.2 1.0 N C:PHE340 3.2 40.5 1.0 CB C:PHE340 3.4 44.1 1.0 C8 C:OLF2 3.6 29.8 1.0 CD2 C:LEU352 3.6 48.0 1.0 C5 C:OLF2 3.6 29.9 1.0 CD2 C:PHE340 3.8 51.5 1.0 CG2 C:ILE339 3.8 40.1 1.0 O C:SER336 3.8 30.9 1.0 C C:ILE339 3.8 42.1 1.0 CD1 C:ILE356 3.9 42.8 1.0 CG C:PHE340 4.0 47.3 1.0 C4 C:OLF2 4.1 29.1 1.0 O C:ILE339 4.2 41.7 1.0 CB C:ILE339 4.3 39.8 1.0 CG C:LEU352 4.3 45.1 1.0 CD1 C:LEU352 4.6 45.3 1.0 C C:PHE340 4.6 44.6 1.0 CA C:ILE339 4.6 36.6 1.0 C C:SER336 4.8 30.9 1.0 CG2 C:THR274 4.9 57.5 1.0 N3 C:OLF2 4.9 29.8 1.0 CE2 C:PHE340 5.0 52.7 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