Fluorine in PDB 3oof: Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)Benzoic 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)Benzoic Acid, PDB code: 3oof 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)	26.82 / 2.29
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.580, 83.340, 190.420, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 25.5

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)Benzoic 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)Benzoic Acid (pdb code 3oof). 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)Benzoic Acid, PDB code: 3oof:
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)Benzoic 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)Benzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:31.1 occ:1.00 F24 A:OOF1 0.0 31.1 1.0 C11 A:OOF1 1.4 33.6 1.0 C13 A:OOF1 2.4 33.6 1.0 C8 A:OOF1 2.4 31.7 1.0 F25 A:OOF1 2.6 38.8 1.0 CG2 A:ILE339 3.2 39.3 1.0 CD1 A:ILE277 3.2 47.7 1.0 CG2 A:THR274 3.6 61.6 1.0 C4 A:OOF1 3.6 28.4 1.0 C9 A:OOF1 3.7 29.4 1.0 CG2 A:ILE273 3.8 55.0 1.0 CD1 A:LEU352 3.9 41.9 1.0 C5 A:OOF1 4.2 28.9 1.0 CD1 A:ILE356 4.3 45.2 1.0 CB A:ILE339 4.3 39.3 1.0 CD2 A:LEU352 4.4 46.2 1.0 CG A:LEU352 4.6 42.5 1.0 CG1 A:ILE277 4.7 51.9 1.0 CB A:THR274 4.8 63.9 1.0 N A:THR274 4.8 52.6 1.0 CB A:ILE273 4.8 55.7 1.0 CA A:THR274 4.8 53.3 1.0 N A:PHE340 4.9 37.5 1.0 N1 A:OOF1 4.9 32.7 1.0 C A:ILE273 5.0 55.6 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)Benzoic 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)Benzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:38.8 occ:1.00 F25 A:OOF1 0.0 38.8 1.0 C13 A:OOF1 1.3 33.6 1.0 C11 A:OOF1 2.3 33.6 1.0 C9 A:OOF1 2.4 29.4 1.0 F24 A:OOF1 2.6 31.1 1.0 CA A:PHE340 3.1 38.2 1.0 CB A:PHE340 3.2 41.1 1.0 N A:PHE340 3.3 37.5 1.0 CD2 A:LEU352 3.5 46.2 1.0 CD1 A:PHE340 3.6 51.2 1.0 C5 A:OOF1 3.6 28.9 1.0 C8 A:OOF1 3.6 31.7 1.0 CD1 A:ILE356 3.6 45.2 1.0 O A:SER336 3.7 34.1 1.0 CG A:PHE340 3.9 45.2 1.0 CG2 A:ILE339 3.9 39.3 1.0 C A:ILE339 4.1 41.2 1.0 C4 A:OOF1 4.1 28.4 1.0 CG A:LEU352 4.2 42.5 1.0 CD1 A:LEU352 4.3 41.9 1.0 CB A:ILE339 4.4 39.3 1.0 C A:PHE340 4.6 42.2 1.0 O A:ILE339 4.6 42.5 1.0 CG2 A:THR274 4.7 61.6 1.0 C A:SER336 4.7 33.4 1.0 CE1 A:PHE340 4.8 52.3 1.0 CA A:ILE339 4.9 35.7 1.0 N3 A:OOF1 4.9 25.3 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)Benzoic 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)Benzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:F2 b:38.3 occ:1.00 F24 C:OOF2 0.0 38.3 1.0 C11 C:OOF2 1.4 34.5 1.0 C8 C:OOF2 2.4 34.7 1.0 C13 C:OOF2 2.4 35.4 1.0 F25 C:OOF2 2.8 40.4 1.0 CG2 C:ILE339 3.1 28.4 1.0 CG2 C:ILE273 3.4 46.6 1.0 C4 C:OOF2 3.6 34.4 1.0 C9 C:OOF2 3.7 34.9 1.0 CD1 C:ILE277 3.7 35.0 1.0 CG2 C:THR274 3.8 40.0 1.0 CD1 C:LEU352 4.1 36.0 1.0 CB C:ILE339 4.1 30.5 1.0 C5 C:OOF2 4.1 33.5 1.0 CD2 C:LEU352 4.6 34.6 1.0 CB C:ILE273 4.7 47.8 1.0 N C:THR274 4.7 43.7 1.0 CD1 C:ILE356 4.7 40.8 1.0 CA C:THR274 4.7 44.5 1.0 CB C:THR274 4.8 43.9 1.0 CG C:LEU352 4.9 37.8 1.0 C C:ILE273 4.9 48.0 1.0 N1 C:OOF2 4.9 33.4 1.0 N C:PHE340 4.9 32.2 1.0 C C:ILE339 4.9 34.1 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)Benzoic 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)Benzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:F2 b:40.4 occ:1.00 F25 C:OOF2 0.0 40.4 1.0 C13 C:OOF2 1.3 35.4 1.0 C9 C:OOF2 2.3 34.9 1.0 C11 C:OOF2 2.4 34.5 1.0 F24 C:OOF2 2.8 38.3 1.0 CA C:PHE340 2.9 32.9 1.0 N C:PHE340 3.0 32.2 1.0 CB C:PHE340 3.1 34.5 1.0 O C:SER336 3.4 30.5 1.0 CD1 C:PHE340 3.5 37.9 1.0 C5 C:OOF2 3.6 33.5 1.0 C8 C:OOF2 3.7 34.7 1.0 C C:ILE339 3.7 34.1 1.0 CG2 C:ILE339 3.8 28.4 1.0 CG C:PHE340 3.8 35.8 1.0 CD2 C:LEU352 3.8 34.6 1.0 CD1 C:ILE356 3.8 40.8 1.0 C4 C:OOF2 4.1 34.4 1.0 CB C:ILE339 4.1 30.5 1.0 O C:ILE339 4.2 35.0 1.0 CG C:LEU352 4.3 37.8 1.0 C C:PHE340 4.4 40.6 1.0 CD1 C:LEU352 4.5 36.0 1.0 CA C:ILE339 4.5 29.2 1.0 C C:SER336 4.5 30.3 1.0 CE1 C:PHE340 4.7 38.3 1.0 N3 C:OOF2 4.9 33.6 1.0 O C:PHE340 4.9 42.7 1.0 CG2 C:THR274 4.9 40.0 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