Fluorine in PDB 5q1b: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q1b 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)	33.66 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.090, 83.580, 187.990, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 23.6

The binding sites of Fluorine atom in the Ligand Binding to Farnesoid-X-Receptor (pdb code 5q1b). 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: 5q1b:
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:54.0 occ:1.00 F33 A:9N7501 0.0 54.0 1.0 C15 A:9N7501 1.3 49.2 1.0 C13 A:9N7501 2.4 48.6 1.0 C10 A:9N7501 2.4 46.8 1.0 F32 A:9N7501 2.7 52.4 1.0 CA A:PHE340 3.2 53.9 1.0 CB A:PHE340 3.3 55.4 1.0 N A:PHE340 3.4 51.2 1.0 CD1 A:PHE340 3.5 62.7 1.0 CD2 A:LEU352 3.6 63.2 1.0 C5 A:9N7501 3.6 43.0 1.0 C8 A:9N7501 3.6 46.5 1.0 CD1 A:ILE356 3.6 50.6 1.0 O A:SER336 3.7 46.5 1.0 CG A:PHE340 3.9 59.4 1.0 CG2 A:ILE339 4.0 52.2 1.0 C A:ILE339 4.0 53.5 1.0 C4 A:9N7501 4.1 42.9 1.0 CG A:LEU352 4.3 62.1 1.0 CB A:ILE339 4.5 50.4 1.0 O A:ILE339 4.6 54.1 1.0 C A:PHE340 4.6 61.1 1.0 CD1 A:LEU352 4.6 62.3 1.0 CE1 A:PHE340 4.7 66.5 1.0 C A:SER336 4.8 44.0 1.0 CA A:ILE339 4.9 48.3 1.0 CG1 A:ILE356 4.9 50.8 1.0 N3 A:9N7501 4.9 42.7 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:52.4 occ:1.00 F32 A:9N7501 0.0 52.4 1.0 C13 A:9N7501 1.4 48.6 1.0 C8 A:9N7501 2.3 46.5 1.0 C15 A:9N7501 2.4 49.2 1.0 F33 A:9N7501 2.7 54.0 1.0 CD1 A:ILE277 3.4 76.7 1.0 CG2 A:ILE339 3.4 52.2 1.0 C4 A:9N7501 3.6 42.9 1.0 C10 A:9N7501 3.6 46.8 1.0 CD1 A:LEU352 3.8 62.3 1.0 CG2 A:THR274 3.9 58.8 1.0 CG2 A:ILE273 4.0 55.4 1.0 C5 A:9N7501 4.1 43.0 1.0 CD2 A:LEU352 4.2 63.2 1.0 CD1 A:ILE356 4.3 50.6 1.0 CG A:LEU352 4.4 62.1 1.0 CB A:ILE339 4.5 50.4 1.0 CA A:THR274 4.7 60.6 1.0 CG1 A:ILE277 4.8 72.6 1.0 N1 A:9N7501 4.9 45.8 1.0 N A:THR274 4.9 58.8 1.0 CB A:THR274 4.9 63.2 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:47.5 occ:1.00 F33 C:9N7501 0.0 47.5 1.0 C15 C:9N7501 1.4 44.8 1.0 C10 C:9N7501 2.4 41.4 1.0 C13 C:9N7501 2.4 43.0 1.0 F32 C:9N7501 2.7 44.0 1.0 CB C:PHE340 3.2 61.1 1.0 CA C:PHE340 3.2 59.8 1.0 N C:PHE340 3.3 58.3 1.0 CD1 C:PHE340 3.4 70.4 1.0 O C:SER336 3.6 49.9 1.0 C5 C:9N7501 3.6 40.2 1.0 C8 C:9N7501 3.6 39.0 1.0 CD1 C:ILE356 3.7 70.2 1.0 CG C:PHE340 3.7 65.2 1.0 CD2 C:LEU352 3.8 65.0 1.0 C4 C:9N7501 4.1 40.2 1.0 C C:ILE339 4.1 63.0 1.0 CG2 C:ILE339 4.2 60.3 1.0 CG C:LEU352 4.5 64.3 1.0 CB C:ILE339 4.5 58.2 1.0 CE1 C:PHE340 4.6 73.1 1.0 C C:PHE340 4.6 66.0 1.0 C C:SER336 4.6 49.5 1.0 O C:ILE339 4.7 65.2 1.0 CA C:ILE339 4.9 55.6 1.0 N3 C:9N7501 4.9 39.5 1.0 CD1 C:LEU352 4.9 64.2 1.0 CG1 C:ILE356 5.0 62.9 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:44.0 occ:1.00 F32 C:9N7501 0.0 44.0 1.0 C13 C:9N7501 1.4 43.0 1.0 C8 C:9N7501 2.4 39.0 1.0 C15 C:9N7501 2.4 44.8 1.0 F33 C:9N7501 2.7 47.5 1.0 CG2 C:ILE339 3.3 60.3 1.0 C4 C:9N7501 3.6 40.2 1.0 CD1 C:ILE277 3.6 82.5 1.0 C10 C:9N7501 3.6 41.4 1.0 CD1 C:LEU352 4.1 64.2 1.0 CG2 C:ILE273 4.1 69.1 1.0 CG2 C:THR274 4.1 77.8 1.0 C5 C:9N7501 4.1 40.2 1.0 CD1 C:ILE356 4.2 70.2 1.0 CD2 C:LEU352 4.3 65.0 1.0 CB C:ILE339 4.3 58.2 1.0 CG C:LEU352 4.5 64.3 1.0 N1 C:9N7501 4.9 44.2 1.0 N C:PHE340 4.9 58.3 1.0 CA C:THR274 5.0 74.8 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