Fluorine in PDB 5q1f: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q1f 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)	35.70 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.686, 84.914, 189.974, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 24.5

The binding sites of Fluorine atom in the Ligand Binding to Farnesoid-X-Receptor (pdb code 5q1f). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q1f:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 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:37.6 occ:1.00 F29 A:9NJ501 0.0 37.6 1.0 C21 A:9NJ501 1.4 33.5 1.0 C14 A:9NJ501 2.3 30.6 1.0 C27 A:9NJ501 2.3 34.4 1.0 N A:PHE340 3.0 36.0 1.0 CA A:PHE340 3.1 38.4 1.0 O A:SER336 3.3 33.5 1.0 CB A:PHE340 3.3 39.7 1.0 C A:ILE339 3.6 38.5 1.0 C5 A:9NJ501 3.6 28.5 1.0 C16 A:9NJ501 3.6 34.0 1.0 CG2 A:ILE339 3.6 34.8 1.0 CB A:ILE339 3.9 34.6 1.0 CD1 A:PHE340 4.0 46.5 1.0 CD2 A:LEU352 4.0 42.4 1.0 C7 A:9NJ501 4.1 32.5 1.0 O A:ILE339 4.1 40.2 1.0 CD1 A:ILE356 4.1 29.5 1.0 CG A:PHE340 4.2 43.0 1.0 CA A:ILE339 4.3 32.6 1.0 C A:SER336 4.4 32.8 1.0 C A:PHE340 4.6 47.3 1.0 CG A:LEU352 4.7 43.0 1.0 CG2 A:THR274 4.7 50.0 1.0 CD1 A:LEU352 4.8 42.0 1.0 N3 A:9NJ501 4.9 30.3 1.0 CA A:SER336 4.9 26.8 1.0

Fluorine binding site 2 out of 2 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 C:F501 b:44.5 occ:1.00 F29 C:9NJ501 0.0 44.5 1.0 C21 C:9NJ501 1.4 42.1 1.0 C14 C:9NJ501 2.3 42.1 1.0 C27 C:9NJ501 2.4 41.5 1.0 N C:PHE340 3.1 47.4 1.0 CA C:PHE340 3.2 48.9 1.0 O C:SER336 3.3 46.0 1.0 CB C:PHE340 3.4 49.4 1.0 C5 C:9NJ501 3.6 42.7 1.0 C16 C:9NJ501 3.6 42.2 1.0 C C:ILE339 3.7 51.2 1.0 CG2 C:ILE339 3.8 50.8 1.0 CD1 C:PHE340 3.9 56.9 1.0 CD1 C:ILE356 4.0 59.9 1.0 CD2 C:LEU352 4.0 54.8 1.0 C7 C:9NJ501 4.1 43.0 1.0 CB C:ILE339 4.1 49.1 1.0 CG C:PHE340 4.1 52.5 1.0 O C:ILE339 4.3 52.6 1.0 C C:SER336 4.4 44.4 1.0 CA C:ILE339 4.5 46.4 1.0 CG C:LEU352 4.6 54.0 1.0 C C:PHE340 4.7 56.2 1.0 CD1 C:LEU352 4.8 54.1 1.0 CG2 C:THR274 4.8 69.2 1.0 N3 C:9NJ501 4.9 44.5 1.0 CA C:SER336 4.9 41.5 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