Fluorine in PDB 5q0v: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q0v 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)	35.39 / 1.87
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.046, 84.832, 189.567, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 23.8

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 5q0v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q0v:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 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:36.0 occ:1.00 F23 A:9LS501 0.0 36.0 1.0 C16 A:9LS501 1.4 29.7 1.0 C14 A:9LS501 2.4 24.1 1.0 C28 A:9LS501 2.4 26.6 1.0 N9 A:9LS501 2.8 24.2 1.0 CD1 A:ILE339 3.2 29.6 1.0 OG A:SER336 3.4 21.1 1.0 C8 A:9LS501 3.5 24.3 1.0 C6 A:9LS501 3.5 25.3 1.0 C32 A:9LS501 3.6 24.7 1.0 C27 A:9LS501 3.6 25.6 1.0 C4 A:9LS501 3.8 21.4 1.0 CA A:SER336 3.9 18.2 1.0 C11 A:9LS501 3.9 25.0 1.0 O15 A:9LS501 3.9 28.8 1.0 CB A:SER336 4.1 20.6 1.0 CG2 A:ILE273 4.1 35.4 1.0 CE A:MET294 4.1 27.2 1.0 C31 A:9LS501 4.1 23.7 1.0 N1 A:9LS501 4.2 21.6 1.0 F20 A:9LS501 4.3 27.6 1.0 N A:SER336 4.4 17.5 1.0 CG1 A:ILE339 4.4 21.1 1.0 C5 A:9LS501 4.4 21.0 1.0 C7 A:9LS501 4.5 23.8 1.0 CB A:ILE339 4.5 21.6 1.0 C13 A:9LS501 4.5 22.9 1.0 CG2 A:ILE339 4.7 21.5 1.0 CD1 A:ILE273 4.8 32.1 1.0 C10 A:9LS501 4.8 23.1 1.0 C A:ARG335 4.8 18.6 1.0 O A:ARG335 4.9 18.8 1.0

Fluorine binding site 2 out of 6 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:24.5 occ:1.00 F21 A:9LS501 0.0 24.5 1.0 C13 A:9LS501 1.3 22.9 1.0 C11 A:9LS501 2.3 25.0 1.0 C10 A:9LS501 2.4 23.1 1.0 F20 A:9LS501 2.7 27.6 1.0 N A:PHE340 3.1 22.1 1.0 CA A:PHE340 3.2 24.2 1.0 CB A:PHE340 3.3 26.0 1.0 CG2 A:ILE339 3.6 21.5 1.0 O A:SER336 3.6 22.4 1.0 C8 A:9LS501 3.6 24.3 1.0 C5 A:9LS501 3.6 21.0 1.0 C A:ILE339 3.7 25.0 1.0 CD2 A:LEU352 3.8 25.5 1.0 CD1 A:PHE340 3.9 36.3 1.0 CD1 A:ILE356 4.0 27.3 1.0 CB A:ILE339 4.0 21.6 1.0 C4 A:9LS501 4.1 21.4 1.0 CG A:PHE340 4.1 30.0 1.0 O A:ILE339 4.3 26.5 1.0 CG A:LEU352 4.5 27.2 1.0 CA A:ILE339 4.5 20.1 1.0 C A:PHE340 4.6 29.0 1.0 CG2 A:THR274 4.7 27.1 1.0 C A:SER336 4.7 22.3 1.0 CD1 A:LEU352 4.7 27.2 1.0 N3 A:9LS501 4.9 21.6 1.0

Fluorine binding site 3 out of 6 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 A:F501 b:27.6 occ:1.00 F20 A:9LS501 0.0 27.6 1.0 C11 A:9LS501 1.4 25.0 1.0 C8 A:9LS501 2.3 24.3 1.0 C13 A:9LS501 2.4 22.9 1.0 F21 A:9LS501 2.7 24.5 1.0 CG2 A:ILE339 3.3 21.5 1.0 CD1 A:ILE277 3.3 36.4 1.0 CG2 A:ILE273 3.5 35.4 1.0 C4 A:9LS501 3.6 21.4 1.0 C10 A:9LS501 3.6 23.1 1.0 CG2 A:THR274 3.7 27.1 1.0 C5 A:9LS501 4.1 21.0 1.0 CD1 A:LEU352 4.1 27.2 1.0 F23 A:9LS501 4.3 36.0 1.0 CB A:ILE339 4.4 21.6 1.0 CD1 A:ILE356 4.6 27.3 1.0 CD2 A:LEU352 4.6 25.5 1.0 CB A:ILE273 4.6 36.6 1.0 N A:THR274 4.6 29.8 1.0 CA A:THR274 4.7 29.8 1.0 C A:ILE273 4.8 33.5 1.0 CB A:THR274 4.8 32.7 1.0 CG1 A:ILE277 4.8 30.9 1.0 CG A:LEU352 4.8 27.2 1.0 N1 A:9LS501 4.9 21.6 1.0

Fluorine binding site 4 out of 6 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:37.9 occ:1.00 F23 C:9LS501 0.0 37.9 1.0 C16 C:9LS501 1.4 34.6 1.0 C14 C:9LS501 2.4 32.1 1.0 C28 C:9LS501 2.4 33.0 1.0 N9 C:9LS501 2.7 33.8 1.0 C6 C:9LS501 3.2 31.8 1.0 OG C:SER336 3.4 25.1 1.0 O15 C:9LS501 3.4 31.7 1.0 CD1 C:ILE339 3.4 30.4 1.0 C32 C:9LS501 3.6 29.6 1.0 C27 C:9LS501 3.6 31.5 1.0 C8 C:9LS501 3.7 25.3 1.0 CE C:MET294 3.9 35.0 1.0 C4 C:9LS501 3.9 24.4 1.0 CA C:SER336 4.0 21.6 1.0 C31 C:9LS501 4.1 30.9 1.0 CB C:SER336 4.2 22.1 1.0 N1 C:9LS501 4.2 28.5 1.0 CG2 C:ILE273 4.2 40.1 1.0 C11 C:9LS501 4.3 27.1 1.0 C7 C:9LS501 4.4 29.9 1.0 N C:SER336 4.5 21.0 1.0 C5 C:9LS501 4.6 24.0 1.0 CG1 C:ILE339 4.7 28.5 1.0 F20 C:9LS501 4.8 28.0 1.0 CB C:ILE339 4.8 29.0 1.0 CD1 C:ILE273 4.9 36.8 1.0 C13 C:9LS501 4.9 25.2 1.0 C2 C:9LS501 4.9 28.0 1.0 C C:ARG335 5.0 25.0 1.0

Fluorine binding site 5 out of 6 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 5 of Ligand Binding to Farnesoid-X-Receptor within 5.0Å range: probe atom residue distance (Å) B Occ C:F501 b:29.6 occ:1.00 F21 C:9LS501 0.0 29.6 1.0 C13 C:9LS501 1.3 25.2 1.0 C11 C:9LS501 2.3 27.1 1.0 C10 C:9LS501 2.4 22.7 1.0 F20 C:9LS501 2.7 28.0 1.0 CA C:PHE340 3.2 30.2 1.0 N C:PHE340 3.2 28.4 1.0 CB C:PHE340 3.3 31.9 1.0 C5 C:9LS501 3.6 24.0 1.0 C8 C:9LS501 3.6 25.3 1.0 CG2 C:ILE339 3.6 29.6 1.0 CD2 C:LEU352 3.7 34.5 1.0 CD1 C:PHE340 3.7 39.8 1.0 O C:SER336 3.8 29.5 1.0 C C:ILE339 3.9 31.6 1.0 CD1 C:ILE356 4.0 30.2 1.0 CG C:PHE340 4.0 35.4 1.0 C4 C:9LS501 4.1 24.4 1.0 CB C:ILE339 4.2 29.0 1.0 O C:ILE339 4.4 32.9 1.0 CG C:LEU352 4.4 33.4 1.0 CG2 C:THR274 4.6 33.5 1.0 CA C:ILE339 4.6 26.8 1.0 C C:PHE340 4.6 35.6 1.0 CD1 C:LEU352 4.6 34.1 1.0 C C:SER336 4.9 27.3 1.0 N3 C:9LS501 4.9 26.4 1.0 CE1 C:PHE340 4.9 41.8 1.0

Fluorine binding site 6 out of 6 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 6 of Ligand Binding to Farnesoid-X-Receptor within 5.0Å range: probe atom residue distance (Å) B Occ C:F501 b:28.0 occ:1.00 F20 C:9LS501 0.0 28.0 1.0 C11 C:9LS501 1.3 27.1 1.0 C8 C:9LS501 2.3 25.3 1.0 C13 C:9LS501 2.4 25.2 1.0 F21 C:9LS501 2.7 29.6 1.0 CG2 C:ILE339 3.3 29.6 1.0 CD1 C:ILE277 3.4 43.2 1.0 C4 C:9LS501 3.6 24.4 1.0 CG2 C:THR274 3.6 33.5 1.0 C10 C:9LS501 3.6 22.7 1.0 CG2 C:ILE273 3.6 40.1 1.0 CD1 C:LEU352 4.0 34.1 1.0 C5 C:9LS501 4.1 24.0 1.0 CD1 C:ILE356 4.4 30.2 1.0 CD2 C:LEU352 4.4 34.5 1.0 CB C:ILE339 4.5 29.0 1.0 N C:THR274 4.6 36.6 1.0 CA C:THR274 4.6 35.7 1.0 CG C:LEU352 4.6 33.4 1.0 CB C:ILE273 4.7 41.1 1.0 CB C:THR274 4.7 39.3 1.0 F23 C:9LS501 4.8 37.9 1.0 C C:ILE273 4.8 41.9 1.0 CG1 C:ILE277 4.8 38.6 1.0 N1 C:9LS501 4.9 28.5 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