Fluorine in PDB 5q18: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q18 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)	27.82 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.234, 82.975, 190.517, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 24

The binding sites of Fluorine atom in the Ligand Binding to Farnesoid-X-Receptor (pdb code 5q18). 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: 5q18:
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:32.4 occ:1.00 F19 A:9MY501 0.0 32.4 1.0 C13 A:9MY501 1.4 30.8 1.0 C12 A:9MY501 2.4 31.8 1.0 C10 A:9MY501 2.4 29.0 1.0 F18 A:9MY501 2.7 33.7 1.0 CA A:PHE340 3.2 30.3 1.0 N A:PHE340 3.2 28.5 1.0 CB A:PHE340 3.4 31.8 1.0 CD2 A:LEU352 3.6 44.1 1.0 C5 A:9MY501 3.6 27.5 1.0 C8 A:9MY501 3.6 29.1 1.0 CG2 A:ILE339 3.7 27.1 1.0 CD1 A:PHE340 3.8 38.8 1.0 C A:ILE339 3.8 30.5 1.0 O A:SER336 3.8 24.8 1.0 C4 A:9MY501 4.1 27.6 1.0 CG A:PHE340 4.1 35.9 1.0 CD1 A:ILE356 4.1 51.3 1.0 CB A:ILE339 4.2 26.3 1.0 CG A:LEU352 4.3 45.1 1.0 O A:ILE339 4.3 30.1 1.0 CD1 A:LEU352 4.5 43.6 1.0 C A:PHE340 4.6 37.3 1.0 CG2 A:THR274 4.6 35.1 1.0 CA A:ILE339 4.6 24.5 1.0 N3 A:9MY501 4.9 27.9 1.0 C A:SER336 4.9 24.0 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:33.7 occ:1.00 F18 A:9MY501 0.0 33.7 1.0 C12 A:9MY501 1.3 31.8 1.0 C13 A:9MY501 2.3 30.8 1.0 C8 A:9MY501 2.4 29.1 1.0 F19 A:9MY501 2.7 32.4 1.0 CD1 A:ILE277 3.4 52.9 1.0 CG2 A:ILE273 3.5 39.6 1.0 C4 A:9MY501 3.6 27.6 1.0 C10 A:9MY501 3.6 29.0 1.0 CG2 A:ILE339 3.7 27.1 1.0 CG2 A:THR274 3.7 35.1 1.0 CD1 A:LEU352 3.9 43.6 1.0 C5 A:9MY501 4.1 27.5 1.0 CD2 A:LEU352 4.4 44.1 1.0 N A:THR274 4.5 35.6 1.0 CA A:THR274 4.5 36.3 1.0 CG A:LEU352 4.6 45.1 1.0 CB A:ILE273 4.6 39.7 1.0 C A:ILE273 4.6 37.9 1.0 CB A:THR274 4.7 41.5 1.0 CG1 A:ILE277 4.7 48.9 1.0 CB A:ILE339 4.7 26.3 1.0 CD1 A:ILE356 4.8 51.3 1.0 O A:ILE273 4.8 36.5 1.0 N1 A:9MY501 4.9 29.2 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:34.0 occ:1.00 F19 C:9MY501 0.0 34.0 1.0 C13 C:9MY501 1.3 28.6 1.0 C10 C:9MY501 2.3 26.7 1.0 C12 C:9MY501 2.4 29.1 1.0 F18 C:9MY501 2.7 32.3 1.0 CA C:PHE340 3.2 30.9 1.0 N C:PHE340 3.3 29.8 1.0 CB C:PHE340 3.5 31.9 1.0 C5 C:9MY501 3.6 25.2 1.0 CD2 C:LEU352 3.6 42.9 1.0 C8 C:9MY501 3.6 26.2 1.0 CG2 C:ILE339 3.7 31.4 1.0 CD1 C:PHE340 3.8 38.7 1.0 O C:SER336 3.9 27.8 1.0 C C:ILE339 4.0 34.6 1.0 CD1 C:ILE356 4.0 45.4 1.0 C4 C:9MY501 4.1 24.0 1.0 CG C:PHE340 4.1 35.1 1.0 CB C:ILE339 4.3 31.1 1.0 CG C:LEU352 4.3 41.3 1.0 O C:ILE339 4.4 35.6 1.0 CD1 C:LEU352 4.5 41.3 1.0 CG2 C:THR274 4.6 42.5 1.0 C C:PHE340 4.7 37.0 1.0 CA C:ILE339 4.7 29.6 1.0 N3 C:9MY501 4.9 25.2 1.0 C C:SER336 5.0 27.8 1.0 CE1 C:PHE340 5.0 41.1 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:32.3 occ:1.00 F18 C:9MY501 0.0 32.3 1.0 C12 C:9MY501 1.4 29.1 1.0 C13 C:9MY501 2.4 28.6 1.0 C8 C:9MY501 2.4 26.2 1.0 F19 C:9MY501 2.7 34.0 1.0 CD1 C:ILE277 3.3 48.5 1.0 CG2 C:ILE273 3.4 42.2 1.0 C4 C:9MY501 3.6 24.0 1.0 C10 C:9MY501 3.6 26.7 1.0 CG2 C:ILE339 3.8 31.4 1.0 CG2 C:THR274 3.8 42.5 1.0 CD1 C:LEU352 3.9 41.3 1.0 C5 C:9MY501 4.1 25.2 1.0 N C:THR274 4.4 39.7 1.0 CD2 C:LEU352 4.5 42.9 1.0 CA C:THR274 4.5 40.3 1.0 CB C:ILE273 4.5 43.2 1.0 C C:ILE273 4.6 44.1 1.0 CG C:LEU352 4.6 41.3 1.0 CG1 C:ILE277 4.7 41.6 1.0 CD1 C:ILE356 4.7 45.4 1.0 O C:ILE273 4.7 43.5 1.0 CB C:THR274 4.8 47.3 1.0 CB C:ILE339 4.9 31.1 1.0 N1 C:9MY501 4.9 23.9 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