Fluorine in PDB 5q15: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q15 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)	12.56 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.032, 84.119, 191.953, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 25.5

The binding sites of Fluorine atom in the Ligand Binding to Farnesoid-X-Receptor (pdb code 5q15). 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: 5q15:
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:39.8 occ:1.00 F20 A:9MP501 0.0 39.8 1.0 C2 A:9MP501 1.4 36.5 1.0 C3 A:9MP501 2.3 34.5 1.0 C1 A:9MP501 2.4 33.4 1.0 F19 A:9MP501 2.7 36.5 1.0 CD1 A:ILE277 3.4 57.1 1.0 CG2 A:ILE273 3.5 43.0 1.0 CG2 A:ILE339 3.6 33.0 1.0 C4 A:9MP501 3.6 32.6 1.0 C6 A:9MP501 3.6 30.7 1.0 CG2 A:THR274 3.7 43.6 1.0 CD1 A:LEU352 4.0 46.8 1.0 C5 A:9MP501 4.1 31.7 1.0 CD2 A:LEU352 4.4 47.9 1.0 N A:THR274 4.5 43.0 1.0 CA A:THR274 4.5 43.3 1.0 CD1 A:ILE356 4.6 41.6 1.0 CG A:LEU352 4.6 47.4 1.0 CB A:ILE273 4.6 43.9 1.0 CB A:ILE339 4.6 30.6 1.0 C A:ILE273 4.7 46.2 1.0 CB A:THR274 4.7 48.8 1.0 CG1 A:ILE277 4.8 47.8 1.0 O A:ILE273 4.8 46.5 1.0 N8 A:9MP501 4.9 32.5 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:36.5 occ:1.00 F19 A:9MP501 0.0 36.5 1.0 C1 A:9MP501 1.4 33.4 1.0 C2 A:9MP501 2.4 36.5 1.0 C6 A:9MP501 2.4 30.7 1.0 F20 A:9MP501 2.7 39.8 1.0 CA A:PHE340 3.2 32.1 1.0 N A:PHE340 3.2 30.6 1.0 CB A:PHE340 3.4 33.2 1.0 C5 A:9MP501 3.6 31.7 1.0 C3 A:9MP501 3.6 34.5 1.0 CG2 A:ILE339 3.7 33.0 1.0 CD2 A:LEU352 3.7 47.9 1.0 C A:ILE339 3.8 34.5 1.0 O A:SER336 3.8 29.6 1.0 CD1 A:PHE340 3.8 40.4 1.0 CD1 A:ILE356 4.1 41.6 1.0 CG A:PHE340 4.1 36.6 1.0 C4 A:9MP501 4.1 32.6 1.0 CB A:ILE339 4.1 30.6 1.0 O A:ILE339 4.3 36.2 1.0 CG A:LEU352 4.4 47.4 1.0 CA A:ILE339 4.5 29.1 1.0 C A:PHE340 4.6 39.7 1.0 CG2 A:THR274 4.6 43.6 1.0 CD1 A:LEU352 4.7 46.8 1.0 N7 A:9MP501 4.9 31.1 1.0 C A:SER336 4.9 29.3 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:37.2 occ:1.00 F20 C:9MP501 0.0 37.2 1.0 C2 C:9MP501 1.4 34.2 1.0 C1 C:9MP501 2.4 32.4 1.0 C3 C:9MP501 2.4 32.5 1.0 F19 C:9MP501 2.7 35.1 1.0 CD1 C:ILE277 3.3 55.2 1.0 CG2 C:ILE273 3.5 44.2 1.0 C4 C:9MP501 3.6 31.6 1.0 C6 C:9MP501 3.6 28.9 1.0 CG2 C:ILE339 3.7 36.2 1.0 CG2 C:THR274 3.8 38.6 1.0 CD1 C:LEU352 4.0 44.9 1.0 C5 C:9MP501 4.1 30.3 1.0 CD2 C:LEU352 4.4 48.4 1.0 N C:THR274 4.5 40.5 1.0 CA C:THR274 4.5 40.4 1.0 CD1 C:ILE356 4.5 45.0 1.0 CB C:ILE273 4.6 44.4 1.0 CG C:LEU352 4.6 44.8 1.0 C C:ILE273 4.6 45.5 1.0 CG1 C:ILE277 4.7 44.9 1.0 CB C:THR274 4.8 42.9 1.0 O C:ILE273 4.8 46.1 1.0 CB C:ILE339 4.8 33.9 1.0 N8 C:9MP501 4.9 31.6 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:35.1 occ:1.00 F19 C:9MP501 0.0 35.1 1.0 C1 C:9MP501 1.3 32.4 1.0 C2 C:9MP501 2.3 34.2 1.0 C6 C:9MP501 2.4 28.9 1.0 F20 C:9MP501 2.7 37.2 1.0 CA C:PHE340 3.3 34.3 1.0 N C:PHE340 3.3 33.2 1.0 CB C:PHE340 3.5 35.3 1.0 C5 C:9MP501 3.6 30.3 1.0 C3 C:9MP501 3.6 32.5 1.0 CD2 C:LEU352 3.6 48.4 1.0 CG2 C:ILE339 3.7 36.2 1.0 CD1 C:PHE340 3.8 42.9 1.0 C C:ILE339 3.9 37.8 1.0 O C:SER336 3.9 33.2 1.0 CD1 C:ILE356 4.0 45.0 1.0 C4 C:9MP501 4.1 31.6 1.0 CG C:PHE340 4.1 38.6 1.0 CB C:ILE339 4.2 33.9 1.0 CG C:LEU352 4.4 44.8 1.0 O C:ILE339 4.4 40.5 1.0 CG2 C:THR274 4.6 38.6 1.0 CD1 C:LEU352 4.7 44.9 1.0 CA C:ILE339 4.7 31.7 1.0 C C:PHE340 4.7 40.2 1.0 N7 C:9MP501 4.9 31.2 1.0 CE1 C:PHE340 5.0 45.0 1.0 C C:SER336 5.0 31.5 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