Fluorine in PDB 5q0u: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q0u was solved by M.G.Rudolph, J.Benz, D.Burger, R.Thoma, A.Ruf, C.Joseph, B.Kuhn, C.Shao, H.Yang, S.K.Burley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.57 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.900, 84.250, 190.410, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 21.8

The structure of Ligand Binding to Farnesoid-X-Receptor also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Ligand Binding to Farnesoid-X-Receptor (pdb code 5q0u). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q0u:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Ligand Binding to Farnesoid-X-Receptor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ligand Binding to Farnesoid-X-Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:34.7 occ:1.00 F26 A:9LP501 0.0 34.7 1.0 C16 A:9LP501 1.3 30.6 1.0 C15 A:9LP501 2.3 27.6 1.0 C17 A:9LP501 2.3 29.8 1.0 F27 A:9LP501 2.7 31.9 1.0 CG2 A:ILE339 3.3 30.3 1.0 CD1 A:ILE277 3.5 45.1 1.0 CG2 A:ILE273 3.6 44.2 1.0 C12 A:9LP501 3.6 24.9 1.0 C18 A:9LP501 3.6 25.8 1.0 CG2 A:THR274 3.8 37.2 1.0 C11 A:9LP501 4.1 23.9 1.0 CB A:ILE339 4.2 28.9 1.0 CD1 A:LEU352 4.3 40.9 1.0 CB A:ILE273 4.6 46.5 1.0 CD2 A:LEU352 4.7 40.1 1.0 CD1 A:ILE356 4.7 31.6 1.0 N A:THR274 4.8 40.1 1.0 N9 A:9LP501 4.9 28.6 1.0 CA A:THR274 4.9 41.1 1.0 C A:ILE273 4.9 43.9 1.0 CG A:LEU352 4.9 40.2 1.0 CB A:THR274 5.0 44.5 1.0

Fluorine binding site 2 out of 4 in the Ligand Binding to Farnesoid-X-Receptor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ligand Binding to Farnesoid-X-Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:31.9 occ:1.00 F27 A:9LP501 0.0 31.9 1.0 C15 A:9LP501 1.3 27.6 1.0 C16 A:9LP501 2.3 30.6 1.0 C18 A:9LP501 2.4 25.8 1.0 F26 A:9LP501 2.7 34.7 1.0 CA A:PHE340 3.1 29.4 1.0 N A:PHE340 3.1 27.4 1.0 CB A:PHE340 3.3 31.5 1.0 O A:SER336 3.6 26.2 1.0 C17 A:9LP501 3.6 29.8 1.0 C11 A:9LP501 3.6 23.9 1.0 C A:ILE339 3.7 30.9 1.0 CD1 A:PHE340 3.7 39.2 1.0 CD2 A:LEU352 3.8 40.1 1.0 CG2 A:ILE339 3.8 30.3 1.0 CD1 A:ILE356 3.9 31.6 1.0 CG A:PHE340 4.0 34.8 1.0 C12 A:9LP501 4.1 24.9 1.0 CB A:ILE339 4.1 28.9 1.0 O A:ILE339 4.2 31.2 1.0 CG A:LEU352 4.4 40.2 1.0 CA A:ILE339 4.5 27.0 1.0 C A:PHE340 4.5 34.4 1.0 CD1 A:LEU352 4.6 40.9 1.0 C A:SER336 4.7 27.2 1.0 CG2 A:THR274 4.8 37.2 1.0 N14 A:9LP501 4.9 24.7 1.0 CE1 A:PHE340 5.0 41.7 1.0 O A:PHE340 5.0 36.2 1.0

Fluorine binding site 3 out of 4 in the Ligand Binding to Farnesoid-X-Receptor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ligand Binding to Farnesoid-X-Receptor within 5.0Å range: probe atom residue distance (Å) B Occ C:F501 b:44.3 occ:1.00 F26 C:9LP501 0.0 44.3 1.0 C16 C:9LP501 1.3 38.1 1.0 C15 C:9LP501 2.3 36.0 1.0 C17 C:9LP501 2.4 36.7 1.0 F27 C:9LP501 2.7 42.4 1.0 CG2 C:ILE339 3.3 42.5 1.0 CD1 C:ILE277 3.5 61.3 1.0 CG2 C:ILE273 3.5 58.3 1.0 C12 C:9LP501 3.6 31.2 1.0 C18 C:9LP501 3.6 33.8 1.0 CG2 C:THR274 3.7 59.8 1.0 C11 C:9LP501 4.1 31.4 1.0 CD1 C:LEU352 4.2 49.0 1.0 CB C:ILE339 4.3 41.8 1.0 CD2 C:LEU352 4.5 49.7 1.0 CB C:ILE273 4.6 60.2 1.0 CD1 C:ILE356 4.7 47.3 1.0 N C:THR274 4.7 56.3 1.0 CA C:THR274 4.8 56.9 1.0 C C:ILE273 4.8 61.4 1.0 CG C:LEU352 4.8 48.6 1.0 N9 C:9LP501 4.9 36.0 1.0 CB C:THR274 4.9 64.2 1.0 CG1 C:ILE277 4.9 56.8 1.0 O C:ILE273 5.0 60.7 1.0

Fluorine binding site 4 out of 4 in the Ligand Binding to Farnesoid-X-Receptor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ligand Binding to Farnesoid-X-Receptor within 5.0Å range: probe atom residue distance (Å) B Occ C:F501 b:42.4 occ:1.00 F27 C:9LP501 0.0 42.4 1.0 C15 C:9LP501 1.3 36.0 1.0 C16 C:9LP501 2.3 38.1 1.0 C18 C:9LP501 2.4 33.8 1.0 F26 C:9LP501 2.7 44.3 1.0 CA C:PHE340 3.1 45.1 1.0 N C:PHE340 3.2 43.5 1.0 CB C:PHE340 3.4 46.9 1.0 C11 C:9LP501 3.6 31.4 1.0 C17 C:9LP501 3.6 36.7 1.0 CD2 C:LEU352 3.6 49.7 1.0 CD1 C:PHE340 3.6 57.0 1.0 O C:SER336 3.7 39.0 1.0 C C:ILE339 3.8 46.0 1.0 CG2 C:ILE339 3.8 42.5 1.0 CD1 C:ILE356 3.9 47.3 1.0 CG C:PHE340 4.0 51.5 1.0 C12 C:9LP501 4.1 31.2 1.0 CB C:ILE339 4.2 41.8 1.0 CG C:LEU352 4.3 48.6 1.0 O C:ILE339 4.3 46.7 1.0 CD1 C:LEU352 4.5 49.0 1.0 C C:PHE340 4.6 51.7 1.0 CA C:ILE339 4.6 40.0 1.0 CG2 C:THR274 4.8 59.8 1.0 C C:SER336 4.8 37.4 1.0 CE1 C:PHE340 4.8 59.6 1.0 N14 C:9LP501 4.9 34.7 1.0

Z.Gaieb, S.Liu, S.Gathiaka, M.Chiu, H.Yang, C.Shao, V.A.Feher, W.P.Walters, B.Kuhn, M.G.Rudolph, S.K.Burley, M.K.Gilson, R.E.Amaro. D3R Grand Challenge 2: Blind Prediction of Protein-Ligand Poses, Affinity Rankings, and Relative Binding Free Energies. J. Comput. Aided Mol. Des. V. 32 1 2018.
ISSN: ISSN 1573-4951
PubMed: 29204945
DOI: 10.1007/S10822-017-0088-4