Chlorine in PDB 3ook: Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic 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)-3,5-Difluorobenzoic Acid, PDB code: 3ook 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)	38.14 / 2.29
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.477, 83.288, 190.007, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 27.1

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)-3,5-Difluorobenzoic Acid also contains other interesting chemical elements:

Fluorine

(F)

8 atoms

The binding sites of Chlorine 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)-3,5-Difluorobenzoic Acid (pdb code 3ook). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine 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)-3,5-Difluorobenzoic Acid, PDB code: 3ook:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 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)-3,5-Difluorobenzoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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)-3,5-Difluorobenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1 b:39.2 occ:1.00 CL34 A:OOK1 0.0 39.2 1.0 C31 A:OOK1 1.7 35.2 1.0 C33 A:OOK1 2.7 31.9 1.0 C32 A:OOK1 2.7 32.4 1.0 CD2 A:LEU455 3.8 45.8 1.0 CZ A:PHE333 3.8 31.2 1.0 C24 A:OOK1 4.0 31.5 1.0 SD A:MET454 4.0 60.5 1.0 C25 A:OOK1 4.0 30.6 1.0 CG A:MET454 4.1 55.2 1.0 CB A:MET454 4.1 50.1 1.0 CD2 A:LEU291 4.2 33.2 1.0 CH2 A:TRP473 4.4 45.3 1.0 CD1 A:LEU291 4.4 26.6 1.0 CZ3 A:TRP458 4.4 33.8 1.0 CE1 A:PHE333 4.4 31.9 1.0 C17 A:OOK1 4.5 30.3 1.0 CD1 A:ILE361 4.5 47.9 1.0 CZ3 A:TRP473 4.6 44.2 1.0 CE2 A:PHE333 4.8 33.3 1.0 CG A:LEU291 4.9 28.6 1.0 CE3 A:TRP458 5.0 32.5 1.0 C A:MET454 5.0 45.1 1.0

Chlorine binding site 2 out of 2 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)-3,5-Difluorobenzoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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)-3,5-Difluorobenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl2 b:42.3 occ:1.00 CL34 C:OOK2 0.0 42.3 1.0 C31 C:OOK2 1.7 40.7 1.0 C32 C:OOK2 2.7 38.6 1.0 C33 C:OOK2 2.7 39.3 1.0 CZ C:PHE333 3.7 32.1 1.0 C25 C:OOK2 4.0 36.5 1.0 C24 C:OOK2 4.0 37.4 1.0 CD2 C:LEU291 4.1 38.4 1.0 CD2 C:LEU455 4.2 48.5 1.0 CZ3 C:TRP458 4.2 39.8 1.0 CD1 C:ILE361 4.2 51.2 1.0 SD C:MET454 4.3 56.7 1.0 CE1 C:PHE333 4.4 34.4 1.0 C17 C:OOK2 4.5 36.1 1.0 CG C:MET454 4.5 52.4 1.0 CE2 C:PHE333 4.6 34.4 1.0 CD1 C:LEU291 4.7 33.5 1.0 CG C:LEU455 4.7 46.3 1.0 CE C:MET332 4.9 45.3 1.0 CE3 C:TRP458 4.9 38.1 1.0 CB C:MET454 4.9 48.3 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