Fluorine in PDB 5q14: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q14 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)	37.00 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.060, 84.460, 191.880, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.7

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 5q14). 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: 5q14:
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:35.0 occ:1.00 F27 A:9MM501 0.0 35.0 1.0 C15 A:9MM501 1.4 29.0 1.0 C16 A:9MM501 2.3 26.7 1.0 C17 A:9MM501 2.3 24.8 1.0 O18 A:9MM501 2.6 23.4 1.0 C6 A:9MM501 3.1 20.9 1.0 C4 A:9MM501 3.1 18.3 1.0 OG A:SER336 3.2 28.9 1.0 C14 A:9MM501 3.3 19.5 1.0 N1 A:9MM501 3.5 21.6 1.0 C9 A:9MM501 3.6 22.4 1.0 C13 A:9MM501 3.6 23.5 1.0 C21 A:9MM501 3.6 27.4 1.0 C5 A:9MM501 3.6 19.4 1.0 CD1 A:ILE339 3.7 30.1 1.0 CA A:SER336 3.7 16.6 1.0 CB A:SER336 3.8 21.0 1.0 C7 A:9MM501 4.0 20.9 1.0 C12 A:9MM501 4.0 22.1 1.0 C8 A:9MM501 4.1 21.1 1.0 C20 A:9MM501 4.1 24.7 1.0 C2 A:9MM501 4.2 21.9 1.0 CG2 A:ILE273 4.3 32.6 1.0 N3 A:9MM501 4.3 21.9 1.0 F25 A:9MM501 4.3 25.2 1.0 CE A:MET294 4.4 26.5 1.0 N A:SER336 4.5 15.6 1.0 CB A:ILE339 4.7 20.1 1.0 CG1 A:ILE339 4.8 20.7 1.0 C10 A:9MM501 4.8 25.1 1.0 CG2 A:ILE339 4.8 22.9 1.0 C A:SER336 4.9 21.2 1.0 O A:SER336 4.9 19.1 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:23.4 occ:1.00 F26 A:9MM501 0.0 23.4 1.0 C12 A:9MM501 1.3 22.1 1.0 C9 A:9MM501 2.3 22.4 1.0 C8 A:9MM501 2.4 21.1 1.0 F25 A:9MM501 2.7 25.2 1.0 N A:PHE340 3.2 18.5 1.0 CA A:PHE340 3.2 20.3 1.0 CB A:PHE340 3.3 22.3 1.0 CG2 A:ILE339 3.6 22.9 1.0 C5 A:9MM501 3.6 19.4 1.0 C6 A:9MM501 3.6 20.9 1.0 O A:SER336 3.7 19.1 1.0 C A:ILE339 3.7 22.2 1.0 CD2 A:LEU352 3.8 25.4 1.0 CD1 A:PHE340 3.8 31.5 1.0 CB A:ILE339 4.0 20.1 1.0 CG A:PHE340 4.1 26.2 1.0 CD1 A:ILE356 4.1 19.1 1.0 C4 A:9MM501 4.1 18.3 1.0 O A:ILE339 4.2 21.6 1.0 CG A:LEU352 4.5 26.6 1.0 CA A:ILE339 4.5 17.2 1.0 C A:PHE340 4.6 26.1 1.0 C A:SER336 4.7 21.2 1.0 CD1 A:LEU352 4.8 26.8 1.0 CG2 A:THR274 4.8 28.8 1.0 N3 A:9MM501 4.9 21.9 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:25.2 occ:1.00 F25 A:9MM501 0.0 25.2 1.0 C9 A:9MM501 1.4 22.4 1.0 C6 A:9MM501 2.4 20.9 1.0 C12 A:9MM501 2.4 22.1 1.0 F26 A:9MM501 2.7 23.4 1.0 CG2 A:ILE339 3.4 22.9 1.0 CG2 A:ILE273 3.4 32.6 1.0 CD1 A:ILE277 3.5 27.8 1.0 C4 A:9MM501 3.6 18.3 1.0 C8 A:9MM501 3.6 21.1 1.0 CG2 A:THR274 3.8 28.8 1.0 CD1 A:LEU352 4.0 26.8 1.0 C5 A:9MM501 4.1 19.4 1.0 F27 A:9MM501 4.3 35.0 1.0 CD2 A:LEU352 4.4 25.4 1.0 CD1 A:ILE356 4.4 19.1 1.0 CB A:ILE339 4.5 20.1 1.0 CB A:ILE273 4.6 34.3 1.0 CG A:LEU352 4.6 26.6 1.0 N A:THR274 4.6 32.0 1.0 CA A:THR274 4.6 31.5 1.0 C A:ILE273 4.7 36.0 1.0 CB A:THR274 4.8 33.0 1.0 CG1 A:ILE277 4.8 26.7 1.0 O A:ILE273 4.9 35.5 1.0 N1 A:9MM501 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:42.9 occ:1.00 F27 C:9MM501 0.0 42.9 1.0 C15 C:9MM501 1.3 40.4 1.0 C17 C:9MM501 2.3 38.2 1.0 C16 C:9MM501 2.3 36.6 1.0 O18 C:9MM501 2.6 34.6 1.0 OG C:SER336 2.7 31.2 1.0 CG C:MET332 3.0 37.8 1.0 O C:MET332 3.5 23.7 1.0 SD C:MET332 3.5 45.3 1.0 C21 C:9MM501 3.6 38.3 1.0 C13 C:9MM501 3.6 36.0 1.0 CE C:MET332 3.8 40.6 1.0 C24 C:9MM501 3.8 28.1 1.0 CB C:SER336 4.0 24.8 1.0 C14 C:9MM501 4.1 31.9 1.0 C20 C:9MM501 4.1 37.9 1.0 CB C:MET332 4.1 30.6 1.0 C C:MET332 4.2 24.3 1.0 CA C:MET332 4.4 26.0 1.0 C30 C:9MM501 4.5 29.6 1.0 CA C:SER336 4.6 22.6 1.0 N C:SER336 4.6 22.4 1.0 N1 C:9MM501 4.7 26.7 1.0 C2 C:9MM501 4.7 27.4 1.0 C7 C:9MM501 4.7 29.6 1.0 C11 C:9MM501 4.7 26.3 1.0 C10 C:9MM501 4.9 37.5 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:29.4 occ:1.00 F26 C:9MM501 0.0 29.4 1.0 C12 C:9MM501 1.3 26.9 1.0 C9 C:9MM501 2.3 27.2 1.0 C8 C:9MM501 2.4 24.5 1.0 F25 C:9MM501 2.7 28.6 1.0 CA C:PHE340 3.2 27.9 1.0 CB C:PHE340 3.3 29.8 1.0 N C:PHE340 3.4 26.4 1.0 CD1 C:PHE340 3.5 38.3 1.0 CD2 C:LEU352 3.5 35.0 1.0 C5 C:9MM501 3.6 24.5 1.0 C6 C:9MM501 3.6 26.8 1.0 CG2 C:ILE339 3.8 29.7 1.0 CG C:PHE340 3.9 33.4 1.0 CD1 C:ILE356 4.0 28.1 1.0 O C:SER336 4.0 25.9 1.0 C C:ILE339 4.0 30.2 1.0 C4 C:9MM501 4.1 24.9 1.0 CG C:LEU352 4.3 31.8 1.0 CB C:ILE339 4.4 28.9 1.0 O C:ILE339 4.4 30.7 1.0 CD1 C:LEU352 4.6 31.9 1.0 CG2 C:THR274 4.6 34.1 1.0 C C:PHE340 4.7 33.4 1.0 CE1 C:PHE340 4.7 41.0 1.0 CA C:ILE339 4.8 25.6 1.0 N3 C:9MM501 4.9 24.5 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:28.6 occ:1.00 F25 C:9MM501 0.0 28.6 1.0 C9 C:9MM501 1.3 27.2 1.0 C6 C:9MM501 2.3 26.8 1.0 C12 C:9MM501 2.3 26.9 1.0 F26 C:9MM501 2.7 29.4 1.0 CD1 C:ILE277 3.5 39.5 1.0 CG2 C:ILE339 3.5 29.7 1.0 CG2 C:ILE273 3.5 38.4 1.0 C4 C:9MM501 3.6 24.9 1.0 CG2 C:THR274 3.6 34.1 1.0 C8 C:9MM501 3.6 24.5 1.0 CD1 C:LEU352 3.8 31.9 1.0 C5 C:9MM501 4.1 24.5 1.0 CD2 C:LEU352 4.1 35.0 1.0 CD1 C:ILE356 4.3 28.1 1.0 CG C:LEU352 4.4 31.8 1.0 CA C:THR274 4.5 33.7 1.0 N C:THR274 4.5 34.4 1.0 CB C:THR274 4.7 38.8 1.0 C C:ILE273 4.7 38.4 1.0 CB C:ILE339 4.7 28.9 1.0 CB C:ILE273 4.7 38.8 1.0 O C:ILE273 4.8 37.2 1.0 CG1 C:ILE277 4.8 32.6 1.0 N1 C:9MM501 4.8 26.7 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