Fluorine in PDB 5q1c: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q1c 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)	27.25 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.480, 84.460, 190.030, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 26.4

The binding sites of Fluorine atom in the Ligand Binding to Farnesoid-X-Receptor (pdb code 5q1c). 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: 5q1c:
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:44.9 occ:1.00 F23 A:9NA501 0.0 44.9 1.0 C14 A:9NA501 1.4 42.4 1.0 C15 A:9NA501 2.4 40.3 1.0 C11 A:9NA501 2.4 41.1 1.0 F24 A:9NA501 2.7 40.4 1.0 CG2 A:ILE273 3.2 49.5 1.0 CG2 A:ILE339 3.2 34.9 1.0 C4 A:9NA501 3.6 40.4 1.0 C12 A:9NA501 3.6 37.9 1.0 CD1 A:ILE277 3.7 48.1 1.0 CG2 A:THR274 4.0 47.5 1.0 C6 A:9NA501 4.1 37.9 1.0 CB A:ILE339 4.1 34.5 1.0 CB A:ILE273 4.4 50.6 1.0 CD1 A:LEU352 4.4 43.3 1.0 CD2 A:LEU352 4.7 42.9 1.0 N A:THR274 4.8 48.5 1.0 C27 A:9NA501 4.9 38.8 1.0 C A:ILE273 4.9 52.1 1.0 N2 A:9NA501 4.9 41.6 1.0 CD1 A:ILE339 4.9 38.3 1.0 CD1 A:ILE356 4.9 35.2 1.0 CA A:THR274 5.0 49.4 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:40.4 occ:1.00 F24 A:9NA501 0.0 40.4 1.0 C15 A:9NA501 1.4 40.3 1.0 C12 A:9NA501 2.4 37.9 1.0 C14 A:9NA501 2.4 42.4 1.0 F23 A:9NA501 2.7 44.9 1.0 N A:PHE340 3.1 36.7 1.0 CA A:PHE340 3.2 38.9 1.0 O A:SER336 3.3 36.9 1.0 CB A:PHE340 3.3 40.6 1.0 C6 A:9NA501 3.6 37.9 1.0 C11 A:9NA501 3.6 41.1 1.0 C A:ILE339 3.7 38.6 1.0 CG2 A:ILE339 3.8 34.9 1.0 CD1 A:PHE340 3.8 47.7 1.0 CB A:ILE339 4.0 34.5 1.0 CD2 A:LEU352 4.1 42.9 1.0 CG A:PHE340 4.1 44.1 1.0 C4 A:9NA501 4.1 40.4 1.0 CD1 A:ILE356 4.2 35.2 1.0 O A:ILE339 4.2 40.3 1.0 C A:SER336 4.4 35.7 1.0 CA A:ILE339 4.4 32.7 1.0 C A:PHE340 4.7 46.4 1.0 CG A:LEU352 4.8 44.7 1.0 CA A:SER336 4.8 29.1 1.0 N3 A:9NA501 4.9 38.6 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:37.9 occ:1.00 F23 C:9NA501 0.0 37.9 1.0 C14 C:9NA501 1.4 36.8 1.0 C15 C:9NA501 2.4 36.5 1.0 C11 C:9NA501 2.4 34.8 1.0 F24 C:9NA501 2.7 38.5 1.0 CG2 C:ILE273 3.4 55.9 1.0 CG2 C:ILE339 3.4 48.0 1.0 CD1 C:ILE277 3.5 50.5 1.0 C4 C:9NA501 3.6 36.1 1.0 C12 C:9NA501 3.6 34.9 1.0 CG2 C:THR274 4.0 59.6 1.0 C6 C:9NA501 4.1 34.3 1.0 CD1 C:LEU352 4.2 47.2 1.0 CB C:ILE339 4.4 46.1 1.0 CD2 C:LEU352 4.5 46.5 1.0 CB C:ILE273 4.6 56.9 1.0 CD1 C:ILE356 4.6 51.9 1.0 CG C:LEU352 4.8 47.1 1.0 N C:THR274 4.8 55.3 1.0 N2 C:9NA501 4.9 42.5 1.0 CA C:THR274 4.9 56.0 1.0 C C:ILE273 4.9 60.2 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:38.5 occ:1.00 F24 C:9NA501 0.0 38.5 1.0 C15 C:9NA501 1.4 36.5 1.0 C12 C:9NA501 2.4 34.9 1.0 C14 C:9NA501 2.4 36.8 1.0 F23 C:9NA501 2.7 37.9 1.0 CA C:PHE340 3.2 49.8 1.0 N C:PHE340 3.2 47.7 1.0 CB C:PHE340 3.3 51.9 1.0 O C:SER336 3.5 40.1 1.0 C6 C:9NA501 3.6 34.3 1.0 CD1 C:PHE340 3.6 61.4 1.0 C11 C:9NA501 3.6 34.8 1.0 C C:ILE339 3.8 50.4 1.0 CD2 C:LEU352 3.9 46.5 1.0 CG C:PHE340 3.9 56.1 1.0 CG2 C:ILE339 3.9 48.0 1.0 CD1 C:ILE356 3.9 51.9 1.0 C4 C:9NA501 4.1 36.1 1.0 CB C:ILE339 4.2 46.1 1.0 O C:ILE339 4.4 51.2 1.0 C C:SER336 4.6 39.0 1.0 CG C:LEU352 4.6 47.1 1.0 CA C:ILE339 4.6 43.7 1.0 C C:PHE340 4.7 54.8 1.0 CE1 C:PHE340 4.8 63.8 1.0 N3 C:9NA501 4.9 36.4 1.0 CD1 C:LEU352 4.9 47.2 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