Fluorine in PDB 5q0n: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q0n 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)	41.27 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.340, 84.530, 191.100, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.6

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

Chlorine

(Cl)

4 atoms

The binding sites of Fluorine atom in the Ligand Binding to Farnesoid-X-Receptor (pdb code 5q0n). 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: 5q0n:
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:36.1 occ:1.00 F27 A:9L4501 0.0 36.1 1.0 C15 A:9L4501 1.3 33.5 1.0 C11 A:9L4501 2.3 37.0 1.0 C10 A:9L4501 2.4 28.4 1.0 F26 A:9L4501 2.7 42.4 1.0 N A:PHE340 3.1 34.6 1.0 CA A:PHE340 3.2 35.9 1.0 CB A:PHE340 3.3 36.6 1.0 O A:SER336 3.5 32.3 1.0 C5 A:9L4501 3.6 26.3 1.0 C8 A:9L4501 3.6 33.7 1.0 C A:ILE339 3.7 38.5 1.0 CD1 A:PHE340 3.8 41.9 1.0 CG2 A:ILE339 3.9 37.3 1.0 CD2 A:LEU352 3.9 37.5 1.0 CD1 A:ILE356 4.0 30.1 1.0 CG A:PHE340 4.1 38.7 1.0 C4 A:9L4501 4.1 29.6 1.0 CB A:ILE339 4.1 36.9 1.0 O A:ILE339 4.3 39.4 1.0 CA A:ILE339 4.5 33.9 1.0 CG A:LEU352 4.5 41.0 1.0 C A:SER336 4.6 30.3 1.0 C A:PHE340 4.7 43.2 1.0 CD1 A:LEU352 4.9 42.2 1.0 N3 A:9L4501 4.9 29.0 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:42.4 occ:1.00 F26 A:9L4501 0.0 42.4 1.0 C11 A:9L4501 1.4 37.0 1.0 C8 A:9L4501 2.3 33.7 1.0 C15 A:9L4501 2.4 33.5 1.0 F27 A:9L4501 2.7 36.1 1.0 CG2 A:ILE339 3.3 37.3 1.0 CD1 A:ILE277 3.6 34.9 1.0 CG2 A:ILE273 3.6 48.5 1.0 C4 A:9L4501 3.6 29.6 1.0 C10 A:9L4501 3.6 28.4 1.0 CG2 A:THR274 4.0 45.7 1.0 C5 A:9L4501 4.1 26.3 1.0 CB A:ILE339 4.2 36.9 1.0 CD1 A:LEU352 4.4 42.2 1.0 CD1 A:ILE356 4.7 30.1 1.0 CD2 A:LEU352 4.7 37.5 1.0 CB A:ILE273 4.8 49.7 1.0 N1 A:9L4501 4.8 32.1 1.0 N A:THR274 4.9 44.1 1.0 CA A:THR274 5.0 43.8 1.0 C21 A:9L4501 5.0 33.2 1.0 CG A:LEU352 5.0 41.0 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:40.2 occ:1.00 F27 C:9L4501 0.0 40.2 1.0 C15 C:9L4501 1.3 36.5 1.0 C11 C:9L4501 2.3 34.3 1.0 C10 C:9L4501 2.4 36.0 1.0 F26 C:9L4501 2.7 37.0 1.0 CA C:PHE340 3.2 43.1 1.0 CB C:PHE340 3.2 44.8 1.0 N C:PHE340 3.3 41.7 1.0 CD1 C:PHE340 3.6 52.4 1.0 C8 C:9L4501 3.6 34.4 1.0 C5 C:9L4501 3.6 34.4 1.0 CD2 C:LEU352 3.6 43.4 1.0 O C:SER336 3.7 35.0 1.0 CD1 C:ILE356 3.8 43.3 1.0 CG C:PHE340 3.9 48.5 1.0 C C:ILE339 3.9 46.5 1.0 C4 C:9L4501 4.1 34.4 1.0 CG2 C:ILE339 4.1 48.3 1.0 CG C:LEU352 4.3 42.1 1.0 CB C:ILE339 4.4 46.5 1.0 O C:ILE339 4.5 47.6 1.0 C C:PHE340 4.6 49.0 1.0 CD1 C:LEU352 4.7 42.6 1.0 CA C:ILE339 4.8 43.4 1.0 C C:SER336 4.8 35.1 1.0 CE1 C:PHE340 4.8 53.9 1.0 N3 C:9L4501 4.9 36.2 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:37.0 occ:1.00 F26 C:9L4501 0.0 37.0 1.0 C11 C:9L4501 1.4 34.3 1.0 C8 C:9L4501 2.3 34.4 1.0 C15 C:9L4501 2.3 36.5 1.0 F27 C:9L4501 2.7 40.2 1.0 CG2 C:ILE339 3.4 48.3 1.0 C4 C:9L4501 3.6 34.4 1.0 CD1 C:ILE277 3.6 49.1 1.0 C10 C:9L4501 3.6 36.0 1.0 CG2 C:ILE273 3.8 58.2 1.0 CG2 C:THR274 3.9 58.4 1.0 C5 C:9L4501 4.1 34.4 1.0 CD1 C:LEU352 4.2 42.6 1.0 CB C:ILE339 4.3 46.5 1.0 CD2 C:LEU352 4.4 43.4 1.0 CD1 C:ILE356 4.4 43.3 1.0 CG C:LEU352 4.7 42.1 1.0 N1 C:9L4501 4.9 36.0 1.0 N C:THR274 4.9 56.1 1.0 CA C:THR274 4.9 56.0 1.0 CB C:ILE273 4.9 60.7 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