Fluorine in PDB 5q16: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q16 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)	12.65 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.949, 84.566, 190.701, 90.00, 90.00, 90.00
R / Rfree (%)	26.3 / 28.4

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 5q16). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q16:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 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:45.3 occ:1.00 F18 A:9MS501 0.0 45.3 1.0 C2 A:9MS501 1.4 44.5 1.0 C3 A:9MS501 2.3 43.9 1.0 C1 A:9MS501 2.4 42.1 1.0 CG2 A:ILE339 3.1 37.1 1.0 CG2 A:ILE273 3.4 49.2 1.0 C4 A:9MS501 3.6 43.3 1.0 C6 A:9MS501 3.6 41.6 1.0 CD1 A:ILE277 3.7 56.7 1.0 CG2 A:THR274 3.7 49.9 1.0 CB A:ILE339 4.0 35.3 1.0 C5 A:9MS501 4.1 42.1 1.0 CD1 A:LEU352 4.3 53.5 1.0 CB A:ILE273 4.4 49.7 1.0 N A:THR274 4.5 48.0 1.0 CA A:THR274 4.6 48.8 1.0 C A:ILE273 4.7 51.5 1.0 CB A:THR274 4.8 54.9 1.0 CD1 A:ILE339 4.8 40.5 1.0 CD2 A:LEU352 4.8 55.9 1.0 N8 A:9MS501 4.9 44.1 1.0 O A:ILE273 4.9 50.8 1.0 CG1 A:ILE339 5.0 34.8 1.0

Fluorine binding site 2 out of 2 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 C:F501 b:44.8 occ:1.00 F18 C:9MS501 0.0 44.8 1.0 C2 C:9MS501 1.4 45.0 1.0 C3 C:9MS501 2.3 44.9 1.0 C1 C:9MS501 2.4 45.6 1.0 CG2 C:ILE339 3.3 40.5 1.0 CG2 C:ILE273 3.3 49.7 1.0 CD1 C:ILE277 3.4 51.2 1.0 C4 C:9MS501 3.6 45.2 1.0 CG2 C:THR274 3.6 49.9 0.5 C6 C:9MS501 3.6 44.6 1.0 CD1 C:LEU352 4.0 47.8 1.0 C5 C:9MS501 4.1 44.8 1.0 OG1 C:THR274 4.1 56.6 0.5 N C:THR274 4.2 48.6 1.0 CA C:THR274 4.3 48.7 0.5 CA C:THR274 4.3 49.0 0.5 CB C:ILE339 4.3 39.8 1.0 CB C:ILE273 4.3 50.1 1.0 C C:ILE273 4.4 52.9 1.0 CB C:THR274 4.6 52.7 0.5 O C:ILE273 4.6 52.8 1.0 CB C:THR274 4.6 57.1 0.5 CD2 C:LEU352 4.7 50.2 1.0 CG1 C:ILE277 4.8 49.2 1.0 CG2 C:THR274 4.8 55.8 0.5 N8 C:9MS501 4.9 46.8 1.0 CG C:LEU352 4.9 47.6 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