Fluorine in PDB 5q0s: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q0s 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)	47.45 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.169, 84.461, 188.977, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 26

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 5q0s). 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: 5q0s:
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:42.2 occ:1.00 F6 A:9LJ501 0.0 42.2 1.0 C2 A:9LJ501 1.4 39.1 1.0 C3 A:9LJ501 2.4 36.9 1.0 C1 A:9LJ501 2.4 38.2 1.0 F5 A:9LJ501 2.7 40.0 1.0 CG2 A:ILE339 3.4 35.4 1.0 CD1 A:ILE277 3.5 38.3 1.0 C8 A:9LJ501 3.6 35.5 1.0 CG2 A:ILE273 3.6 41.5 1.0 C4 A:9LJ501 3.6 35.7 1.0 CG2 A:THR274 3.8 37.8 1.0 CD1 A:LEU352 4.0 36.5 1.0 C7 A:9LJ501 4.1 34.4 1.0 CB A:ILE339 4.4 34.0 1.0 CB A:ILE273 4.6 41.5 1.0 CD2 A:LEU352 4.6 37.3 1.0 CD1 A:ILE356 4.6 34.9 1.0 N A:THR274 4.6 38.0 1.0 CA A:THR274 4.7 38.8 1.0 CG A:LEU352 4.7 37.8 1.0 C A:ILE273 4.8 41.0 1.0 CB A:THR274 4.9 44.4 1.0 N9 A:9LJ501 4.9 36.5 1.0 CG1 A:ILE277 5.0 39.7 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:40.0 occ:1.00 F5 A:9LJ501 0.0 40.0 1.0 C1 A:9LJ501 1.3 38.2 1.0 C4 A:9LJ501 2.4 35.7 1.0 C2 A:9LJ501 2.4 39.1 1.0 F6 A:9LJ501 2.7 42.2 1.0 CA A:PHE340 3.2 35.6 1.0 N A:PHE340 3.2 35.2 1.0 CB A:PHE340 3.3 37.1 1.0 O A:SER336 3.4 32.2 1.0 C7 A:9LJ501 3.6 34.4 1.0 C3 A:9LJ501 3.6 36.9 1.0 CD1 A:PHE340 3.6 44.4 1.0 CD2 A:LEU352 3.8 37.3 1.0 C A:ILE339 3.8 39.3 1.0 CG2 A:ILE339 3.9 35.4 1.0 CG A:PHE340 4.0 40.6 1.0 CD1 A:ILE356 4.0 34.9 1.0 C8 A:9LJ501 4.1 35.5 1.0 CB A:ILE339 4.2 34.0 1.0 O A:ILE339 4.4 42.1 1.0 CG A:LEU352 4.5 37.8 1.0 C A:SER336 4.5 30.9 1.0 CA A:ILE339 4.6 32.2 1.0 C A:PHE340 4.6 39.9 1.0 CD1 A:LEU352 4.7 36.5 1.0 CG2 A:THR274 4.9 37.8 1.0 CE1 A:PHE340 4.9 47.3 1.0 N11 A:9LJ501 4.9 36.4 1.0 CA A:SER336 5.0 24.9 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:32.1 occ:1.00 F6 C:9LJ501 0.0 32.1 1.0 C2 C:9LJ501 1.3 33.0 1.0 C3 C:9LJ501 2.3 35.8 1.0 C1 C:9LJ501 2.3 34.3 1.0 F5 C:9LJ501 2.7 37.5 1.0 CG2 C:ILE339 3.5 42.7 1.0 CD1 C:ILE277 3.6 45.2 1.0 C8 C:9LJ501 3.6 35.8 1.0 C4 C:9LJ501 3.6 33.1 1.0 CG2 C:ILE273 3.7 50.9 1.0 CG2 C:THR274 3.7 49.5 1.0 CD1 C:LEU352 3.9 42.5 1.0 C7 C:9LJ501 4.1 33.0 1.0 CD2 C:LEU352 4.4 43.9 1.0 CD1 C:ILE356 4.4 44.0 1.0 CB C:ILE339 4.5 42.4 1.0 CB C:ILE273 4.6 51.6 1.0 CG C:LEU352 4.6 42.9 1.0 N C:THR274 4.6 47.6 1.0 CA C:THR274 4.7 47.7 1.0 CB C:THR274 4.8 54.9 1.0 C C:ILE273 4.9 52.6 1.0 N9 C:9LJ501 4.9 38.7 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:37.5 occ:1.00 F5 C:9LJ501 0.0 37.5 1.0 C1 C:9LJ501 1.3 34.3 1.0 C2 C:9LJ501 2.3 33.0 1.0 C4 C:9LJ501 2.4 33.1 1.0 F6 C:9LJ501 2.7 32.1 1.0 CB C:PHE340 3.2 46.3 1.0 CA C:PHE340 3.3 44.1 1.0 N C:PHE340 3.3 42.1 1.0 O C:SER336 3.6 35.2 1.0 C7 C:9LJ501 3.6 33.0 1.0 C3 C:9LJ501 3.6 35.8 1.0 CD2 C:LEU352 3.7 43.9 1.0 CD1 C:PHE340 3.7 55.4 1.0 CD1 C:ILE356 3.9 44.0 1.0 CG C:PHE340 4.0 50.5 1.0 CG2 C:ILE339 4.0 42.7 1.0 C C:ILE339 4.0 45.3 1.0 C8 C:9LJ501 4.1 35.8 1.0 CG C:LEU352 4.3 42.9 1.0 CB C:ILE339 4.4 42.4 1.0 O C:ILE339 4.5 46.5 1.0 CD1 C:LEU352 4.6 42.5 1.0 C C:SER336 4.7 33.6 1.0 C C:PHE340 4.7 47.3 1.0 CA C:ILE339 4.8 39.2 1.0 CG2 C:THR274 4.8 49.5 1.0 N11 C:9LJ501 4.9 33.8 1.0 CE1 C:PHE340 5.0 57.8 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