Fluorine in PDB 5q0p: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q0p 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)	47.54 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.880, 84.860, 190.650, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 25.4

The structure of Ligand Binding to Farnesoid-X-Receptor also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Ligand Binding to Farnesoid-X-Receptor (pdb code 5q0p). 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: 5q0p:
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:25.6 occ:1.00 F23 A:9LA501 0.0 25.6 1.0 C11 A:9LA501 1.3 26.7 1.0 C9 A:9LA501 2.3 26.6 1.0 C8 A:9LA501 2.4 25.1 1.0 F22 A:9LA501 2.7 26.5 1.0 N A:PHE340 3.2 25.0 1.0 CA A:PHE340 3.2 27.3 1.0 CB A:PHE340 3.3 29.9 1.0 C5 A:9LA501 3.6 26.1 1.0 C6 A:9LA501 3.6 26.6 1.0 CG2 A:ILE339 3.6 24.8 1.0 CD2 A:LEU352 3.7 32.3 1.0 CD1 A:PHE340 3.7 40.3 1.0 C A:ILE339 3.7 28.1 1.0 O A:SER336 3.8 27.6 1.0 CG A:PHE340 4.0 34.0 1.0 C4 A:9LA501 4.1 25.1 1.0 CB A:ILE339 4.1 23.7 1.0 CD1 A:ILE356 4.1 26.9 1.0 O A:ILE339 4.3 28.1 1.0 CG A:LEU352 4.4 32.3 1.0 CA A:ILE339 4.5 22.0 1.0 C A:PHE340 4.6 32.6 1.0 CG2 A:THR274 4.7 29.7 1.0 CD1 A:LEU352 4.7 32.2 1.0 C A:SER336 4.9 28.3 1.0 N3 A:9LA501 4.9 26.8 1.0 CE1 A:PHE340 5.0 43.2 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:26.5 occ:1.00 F22 A:9LA501 0.0 26.5 1.0 C9 A:9LA501 1.4 26.6 1.0 C6 A:9LA501 2.4 26.6 1.0 C11 A:9LA501 2.4 26.7 1.0 F23 A:9LA501 2.7 25.6 1.0 CG2 A:ILE339 3.3 24.8 1.0 CD1 A:ILE277 3.5 31.2 1.0 CG2 A:THR274 3.6 29.7 1.0 C4 A:9LA501 3.6 25.1 1.0 CG2 A:ILE273 3.6 27.8 1.0 C8 A:9LA501 3.7 25.1 1.0 CD1 A:LEU352 3.8 32.2 1.0 C5 A:9LA501 4.1 26.1 1.0 CD2 A:LEU352 4.2 32.3 1.0 CD1 A:ILE356 4.4 26.9 1.0 CA A:THR274 4.4 28.9 1.0 CG A:LEU352 4.4 32.3 1.0 N A:THR274 4.5 28.9 1.0 CB A:ILE339 4.5 23.7 1.0 CB A:ILE273 4.6 29.8 1.0 CB A:THR274 4.6 30.4 1.0 C A:ILE273 4.6 31.6 1.0 O A:ILE273 4.8 31.2 1.0 CG1 A:ILE277 4.9 32.2 1.0 N1 A:9LA501 4.9 26.1 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:29.4 occ:1.00 F23 C:9LA501 0.0 29.4 1.0 C11 C:9LA501 1.3 27.1 1.0 C9 C:9LA501 2.3 27.5 1.0 C8 C:9LA501 2.3 25.2 1.0 F22 C:9LA501 2.7 27.9 1.0 CA C:PHE340 3.2 28.0 1.0 CB C:PHE340 3.2 29.6 1.0 N C:PHE340 3.3 26.5 1.0 CD1 C:PHE340 3.4 37.6 1.0 CD2 C:LEU352 3.5 38.5 1.0 C5 C:9LA501 3.6 23.2 1.0 C6 C:9LA501 3.6 26.4 1.0 CG C:PHE340 3.8 32.5 1.0 CG2 C:ILE339 3.9 30.0 1.0 O C:SER336 4.0 28.3 1.0 C C:ILE339 4.0 30.6 1.0 CD1 C:ILE356 4.0 31.1 1.0 C4 C:9LA501 4.1 25.2 1.0 CG C:LEU352 4.3 35.5 1.0 CB C:ILE339 4.4 29.8 1.0 O C:ILE339 4.5 30.2 1.0 CE1 C:PHE340 4.6 39.7 1.0 CG2 C:THR274 4.6 30.8 1.0 C C:PHE340 4.6 33.4 1.0 CD1 C:LEU352 4.7 36.1 1.0 CA C:ILE339 4.8 27.1 1.0 N3 C:9LA501 4.9 23.4 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:27.9 occ:1.00 F22 C:9LA501 0.0 27.9 1.0 C9 C:9LA501 1.3 27.5 1.0 C6 C:9LA501 2.3 26.4 1.0 C11 C:9LA501 2.3 27.1 1.0 F23 C:9LA501 2.7 29.4 1.0 CG2 C:ILE339 3.5 30.0 1.0 CG2 C:THR274 3.5 30.8 1.0 C4 C:9LA501 3.6 25.2 1.0 C8 C:9LA501 3.6 25.2 1.0 CD1 C:ILE277 3.6 32.7 1.0 CD1 C:LEU352 3.7 36.1 1.0 CG2 C:ILE273 3.8 34.2 1.0 CD2 C:LEU352 3.9 38.5 1.0 C5 C:9LA501 4.1 23.2 1.0 CD1 C:ILE356 4.2 31.1 1.0 CG C:LEU352 4.2 35.5 1.0 CA C:THR274 4.4 33.0 1.0 N C:THR274 4.5 33.0 1.0 CB C:THR274 4.5 35.1 1.0 CB C:ILE339 4.6 29.8 1.0 C C:ILE273 4.7 36.5 1.0 CB C:ILE273 4.7 35.1 1.0 O C:ILE273 4.8 35.5 1.0 N1 C:9LA501 4.9 25.5 1.0 CG1 C:ILE277 5.0 29.8 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