Fluorine in PDB 5q0y: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q0y 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)	27.80 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.370, 84.480, 189.680, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 22

The binding sites of Fluorine atom in the Ligand Binding to Farnesoid-X-Receptor (pdb code 5q0y). 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: 5q0y:
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:35.0 occ:1.00 F5 A:9LY501 0.0 35.0 1.0 C1 A:9LY501 1.3 30.5 1.0 C4 A:9LY501 2.3 28.4 1.0 C2 A:9LY501 2.3 32.5 1.0 F6 A:9LY501 2.7 32.9 1.0 N A:PHE340 3.0 31.5 1.0 CA A:PHE340 3.1 33.2 1.0 CB A:PHE340 3.4 34.1 1.0 CG2 A:ILE339 3.5 30.1 1.0 C A:ILE339 3.6 34.1 1.0 O A:SER336 3.6 28.0 1.0 C7 A:9LY501 3.6 27.1 1.0 C3 A:9LY501 3.6 28.1 1.0 CD2 A:LEU352 3.8 35.8 1.0 CB A:ILE339 3.9 28.8 1.0 CD1 A:PHE340 4.0 40.7 1.0 C8 A:9LY501 4.1 27.8 1.0 O A:ILE339 4.1 34.7 1.0 CG A:PHE340 4.2 37.2 1.0 CD1 A:ILE356 4.2 25.4 1.0 CA A:ILE339 4.3 27.1 1.0 CG A:LEU352 4.4 39.5 1.0 C A:PHE340 4.5 41.3 1.0 CG2 A:THR274 4.6 39.0 1.0 CD1 A:LEU352 4.6 39.1 1.0 C A:SER336 4.7 26.8 1.0 N10 A:9LY501 4.9 26.9 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:32.9 occ:1.00 F6 A:9LY501 0.0 32.9 1.0 C2 A:9LY501 1.4 32.5 1.0 C3 A:9LY501 2.4 28.1 1.0 C1 A:9LY501 2.4 30.5 1.0 F5 A:9LY501 2.7 35.0 1.0 CG2 A:ILE339 3.3 30.1 1.0 CD1 A:ILE277 3.4 38.3 1.0 CG2 A:ILE273 3.4 42.1 1.0 C8 A:9LY501 3.6 27.8 1.0 CG2 A:THR274 3.6 39.0 1.0 C4 A:9LY501 3.6 28.4 1.0 CD1 A:LEU352 4.0 39.1 1.0 C7 A:9LY501 4.1 27.1 1.0 CB A:ILE339 4.3 28.8 1.0 N A:THR274 4.5 38.0 1.0 CB A:ILE273 4.5 43.9 1.0 CA A:THR274 4.6 39.3 1.0 CD2 A:LEU352 4.6 35.8 1.0 C A:ILE273 4.7 41.5 1.0 CB A:THR274 4.7 45.1 1.0 CG A:LEU352 4.7 39.5 1.0 CD1 A:ILE356 4.8 25.4 1.0 O A:ILE273 4.9 39.2 1.0 N9 A:9LY501 4.9 28.5 1.0 CG1 A:ILE277 4.9 35.5 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:35.2 occ:1.00 F5 C:9LY501 0.0 35.2 1.0 C1 C:9LY501 1.3 31.1 1.0 C2 C:9LY501 2.3 32.1 1.0 C4 C:9LY501 2.4 28.2 1.0 F6 C:9LY501 2.7 35.5 1.0 CA C:PHE340 3.1 35.8 1.0 N C:PHE340 3.1 34.1 1.0 CB C:PHE340 3.2 37.0 1.0 C7 C:9LY501 3.6 28.5 1.0 C3 C:9LY501 3.6 30.1 1.0 O C:SER336 3.6 36.2 1.0 CG2 C:ILE339 3.7 36.3 1.0 C C:ILE339 3.7 38.3 1.0 CD1 C:PHE340 3.7 45.1 1.0 CD2 C:LEU352 3.7 39.1 1.0 CG C:PHE340 4.0 40.3 1.0 CD1 C:ILE356 4.0 45.6 1.0 C8 C:9LY501 4.1 30.0 1.0 CB C:ILE339 4.1 35.9 1.0 O C:ILE339 4.3 38.8 1.0 CG C:LEU352 4.4 41.2 1.0 CA C:ILE339 4.5 33.8 1.0 C C:PHE340 4.5 41.4 1.0 CD1 C:LEU352 4.6 41.5 1.0 C C:SER336 4.7 34.5 1.0 CG2 C:THR274 4.8 43.3 1.0 N10 C:9LY501 4.9 30.8 1.0 CE1 C:PHE340 5.0 46.6 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:35.5 occ:1.00 F6 C:9LY501 0.0 35.5 1.0 C2 C:9LY501 1.3 32.1 1.0 C1 C:9LY501 2.3 31.1 1.0 C3 C:9LY501 2.3 30.1 1.0 F5 C:9LY501 2.7 35.2 1.0 CG2 C:ILE339 3.3 36.3 1.0 CD1 C:ILE277 3.5 52.0 1.0 C8 C:9LY501 3.6 30.0 1.0 CG2 C:ILE273 3.6 42.9 1.0 C4 C:9LY501 3.6 28.2 1.0 CG2 C:THR274 3.7 43.3 1.0 CD1 C:LEU352 4.0 41.5 1.0 C7 C:9LY501 4.1 28.5 1.0 CB C:ILE339 4.4 35.9 1.0 CD2 C:LEU352 4.5 39.1 1.0 CD1 C:ILE356 4.6 45.6 1.0 CG C:LEU352 4.6 41.2 1.0 N C:THR274 4.7 42.3 1.0 CA C:THR274 4.7 42.2 1.0 CB C:ILE273 4.7 45.0 1.0 CB C:THR274 4.8 49.5 1.0 C C:ILE273 4.8 46.9 1.0 N9 C:9LY501 4.9 32.2 1.0 CG1 C:ILE277 4.9 48.0 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