Fluorine in PDB 3omm: 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-Fluorobenzoic 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-Fluorobenzoic Acid, PDB code: 3omm 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)	47.62 / 2.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.130, 83.940, 190.480, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 25.6

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-Fluorobenzoic 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-Fluorobenzoic Acid (pdb code 3omm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 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-Fluorobenzoic Acid, PDB code: 3omm:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 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-Fluorobenzoic 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-Fluorobenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:43.8 occ:1.00 F26 A:OMM1 0.0 43.8 1.0 C11 A:OMM1 1.4 40.0 1.0 C8 A:OMM1 2.3 37.8 1.0 C15 A:OMM1 2.4 38.3 1.0 F27 A:OMM1 2.7 45.0 1.0 CG2 A:ILE273 3.2 56.1 1.0 CG2 A:ILE339 3.3 42.4 1.0 CG2 A:THR274 3.5 45.2 1.0 C4 A:OMM1 3.6 35.0 1.0 C10 A:OMM1 3.7 37.4 1.0 CD1 A:ILE277 3.8 58.4 1.0 C5 A:OMM1 4.1 33.5 1.0 CD1 A:LEU352 4.2 46.9 1.0 CB A:ILE339 4.3 42.3 1.0 CB A:ILE273 4.5 57.3 1.0 CD2 A:LEU352 4.6 44.1 1.0 CD1 A:ILE356 4.6 41.9 1.0 N A:THR274 4.7 51.4 1.0 CB A:THR274 4.8 52.0 1.0 CG A:LEU352 4.8 48.3 1.0 N1 A:OMM1 4.8 36.4 1.0 CA A:THR274 4.8 51.4 1.0 C A:ILE273 4.9 55.9 1.0 C21 A:OMM1 5.0 48.8 1.0

Fluorine binding site 2 out of 6 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-Fluorobenzoic 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-Fluorobenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:45.0 occ:1.00 F27 A:OMM1 0.0 45.0 1.0 C15 A:OMM1 1.3 38.3 1.0 C10 A:OMM1 2.3 37.4 1.0 C11 A:OMM1 2.3 40.0 1.0 F26 A:OMM1 2.7 43.8 1.0 CA A:PHE340 3.0 43.8 1.0 N A:PHE340 3.1 42.1 1.0 CB A:PHE340 3.2 46.5 1.0 CD1 A:PHE340 3.5 53.7 1.0 O A:SER336 3.6 37.9 1.0 C8 A:OMM1 3.6 37.8 1.0 C5 A:OMM1 3.6 33.5 1.0 C A:ILE339 3.7 44.9 1.0 CD2 A:LEU352 3.7 44.1 1.0 CG A:PHE340 3.8 49.7 1.0 CD1 A:ILE356 3.8 41.9 1.0 CG2 A:ILE339 3.9 42.4 1.0 C4 A:OMM1 4.1 35.0 1.0 O A:ILE339 4.2 46.9 1.0 CB A:ILE339 4.3 42.3 1.0 CG A:LEU352 4.3 48.3 1.0 C A:PHE340 4.5 50.7 1.0 CA A:ILE339 4.6 39.7 1.0 CD1 A:LEU352 4.6 46.9 1.0 C A:SER336 4.7 38.5 1.0 CG2 A:THR274 4.7 45.2 1.0 CE1 A:PHE340 4.7 54.9 1.0 N3 A:OMM1 4.8 33.1 1.0 O A:PHE340 5.0 50.9 1.0

Fluorine binding site 3 out of 6 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-Fluorobenzoic 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-Fluorobenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:61.6 occ:1.00 F28 A:OMM1 0.0 61.6 1.0 C17 A:OMM1 1.3 53.8 1.0 C12 A:OMM1 2.4 46.5 1.0 C18 A:OMM1 2.4 50.8 1.0 N9 A:OMM1 2.8 40.8 1.0 CE A:MET332 3.0 54.3 1.0 C6 A:OMM1 3.2 39.5 1.0 O19 A:OMM1 3.3 42.1 1.0 CB A:MET294 3.3 41.1 1.0 C21 A:OMM1 3.6 48.8 1.0 C16 A:OMM1 3.7 46.4 1.0 SD A:MET332 3.7 56.1 1.0 C A:MET294 3.8 37.9 1.0 N A:ALA295 3.8 34.8 1.0 O A:MET294 4.0 36.0 1.0 C22 A:OMM1 4.1 47.2 1.0 CA A:ALA295 4.1 33.6 1.0 CA A:MET294 4.2 38.1 1.0 CG A:MET294 4.4 46.9 1.0 C7 A:OMM1 4.4 37.6 1.0 CB A:ALA295 4.6 34.2 1.0 OG A:SER336 4.7 32.9 1.0 O A:LEU291 4.8 41.6 1.0 CB A:HIS298 4.8 32.1 1.0 C13 A:OMM1 4.9 47.3 1.0 CD1 A:LEU291 4.9 37.2 1.0 O20 A:OMM1 5.0 40.9 1.0

Fluorine binding site 4 out of 6 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-Fluorobenzoic 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-Fluorobenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:F2 b:46.1 occ:1.00 F26 C:OMM2 0.0 46.1 1.0 C11 C:OMM2 1.4 45.4 1.0 C15 C:OMM2 2.4 43.2 1.0 C8 C:OMM2 2.4 42.4 1.0 F27 C:OMM2 2.7 48.6 1.0 CG2 C:ILE339 3.3 49.8 1.0 CG2 C:THR274 3.5 72.2 1.0 CD1 C:ILE277 3.6 65.2 1.0 C10 C:OMM2 3.6 41.9 1.0 C4 C:OMM2 3.7 40.6 1.0 CG2 C:ILE273 3.8 72.0 1.0 C5 C:OMM2 4.2 40.9 1.0 CD2 C:LEU352 4.2 58.6 1.0 CB C:ILE339 4.3 49.5 1.0 CD1 C:LEU352 4.3 57.5 1.0 CD1 C:ILE356 4.4 49.8 1.0 CG C:LEU352 4.7 57.0 1.0 CB C:THR274 4.7 73.1 1.0 N C:THR274 4.8 66.2 1.0 CB C:ILE273 4.8 72.1 1.0 CA C:THR274 4.8 66.2 1.0 N1 C:OMM2 4.9 45.0 1.0 N C:PHE340 4.9 52.6 1.0 C C:ILE273 4.9 70.2 1.0

Fluorine binding site 5 out of 6 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-Fluorobenzoic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 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-Fluorobenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:F2 b:48.6 occ:1.00 F27 C:OMM2 0.0 48.6 1.0 C15 C:OMM2 1.3 43.2 1.0 C11 C:OMM2 2.3 45.4 1.0 C10 C:OMM2 2.4 41.9 1.0 F26 C:OMM2 2.7 46.1 1.0 CA C:PHE340 3.2 54.6 1.0 CB C:PHE340 3.3 57.6 1.0 N C:PHE340 3.3 52.6 1.0 CD1 C:PHE340 3.5 65.5 1.0 CD2 C:LEU352 3.5 58.6 1.0 C8 C:OMM2 3.6 42.4 1.0 C5 C:OMM2 3.6 40.9 1.0 O C:SER336 3.7 40.0 1.0 CG C:PHE340 3.8 60.9 1.0 CD1 C:ILE356 3.9 49.8 1.0 C C:ILE339 4.0 53.3 1.0 C4 C:OMM2 4.1 40.6 1.0 CG2 C:ILE339 4.1 49.8 1.0 CG C:LEU352 4.4 57.0 1.0 CB C:ILE339 4.4 49.5 1.0 O C:ILE339 4.5 53.5 1.0 C C:PHE340 4.6 59.5 1.0 CE1 C:PHE340 4.7 66.5 1.0 C C:SER336 4.8 40.2 1.0 CA C:ILE339 4.8 46.5 1.0 N3 C:OMM2 4.9 41.0 1.0 CG2 C:THR274 4.9 72.2 1.0 CD1 C:LEU352 4.9 57.5 1.0

Fluorine binding site 6 out of 6 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-Fluorobenzoic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 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-Fluorobenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:F2 b:65.5 occ:1.00 F28 C:OMM2 0.0 65.5 1.0 C17 C:OMM2 1.3 62.7 1.0 C12 C:OMM2 2.4 62.3 1.0 C18 C:OMM2 2.4 59.0 1.0 N9 C:OMM2 2.7 63.3 1.0 SD C:MET332 3.5 64.3 1.0 CG C:MET332 3.6 57.0 1.0 C6 C:OMM2 3.6 59.6 1.0 C21 C:OMM2 3.6 61.9 1.0 C16 C:OMM2 3.6 57.1 1.0 O C:MET294 3.8 43.0 1.0 C C:MET294 3.9 45.9 1.0 CB C:MET294 3.9 49.1 1.0 N C:ALA295 4.0 40.5 1.0 O19 C:OMM2 4.1 59.3 1.0 C22 C:OMM2 4.1 60.9 1.0 CA C:ALA295 4.2 40.7 1.0 OG C:SER336 4.3 37.1 1.0 CA C:MET294 4.5 46.5 1.0 CB C:HIS298 4.5 40.3 1.0 CB C:MET332 4.6 50.6 1.0 CD2 C:LEU291 4.6 48.1 1.0 C7 C:OMM2 4.6 52.5 1.0 CB C:ALA295 4.7 41.3 1.0 C13 C:OMM2 4.9 56.5 1.0 C25 C:OMM2 4.9 43.9 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