Fluorine in PDB 5q1d: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q1d 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)	27.67 / 1.89
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.440, 84.530, 190.540, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24.4

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 5q1d). 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: 5q1d:
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:30.3 occ:1.00 F19 A:9ND501 0.0 30.3 1.0 C13 A:9ND501 1.3 24.8 1.0 C11 A:9ND501 2.3 27.6 1.0 C9 A:9ND501 2.4 20.9 1.0 F18 A:9ND501 2.7 30.8 1.0 CA A:PHE340 3.1 27.5 1.0 N A:PHE340 3.2 25.4 1.0 CB A:PHE340 3.3 29.1 1.0 CD1 A:PHE340 3.6 38.5 1.0 C5 A:9ND501 3.6 21.6 1.0 C8 A:9ND501 3.6 25.9 1.0 CD2 A:LEU352 3.7 37.4 1.0 CG2 A:ILE339 3.7 27.4 1.0 O A:SER336 3.7 28.6 1.0 C A:ILE339 3.8 28.8 1.0 CG A:PHE340 3.9 33.6 1.0 CD1 A:ILE356 4.0 26.1 1.0 C4 A:9ND501 4.1 21.1 1.0 CB A:ILE339 4.1 26.6 1.0 O A:ILE339 4.2 29.6 1.0 CG A:LEU352 4.4 36.0 1.0 C A:PHE340 4.6 34.5 1.0 CA A:ILE339 4.6 24.3 1.0 CD1 A:LEU352 4.7 35.7 1.0 CG2 A:THR274 4.8 31.6 1.0 C A:SER336 4.8 27.3 1.0 CE1 A:PHE340 4.8 41.2 1.0 N3 A:9ND501 4.9 22.0 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:30.8 occ:1.00 F18 A:9ND501 0.0 30.8 1.0 C11 A:9ND501 1.3 27.6 1.0 C8 A:9ND501 2.3 25.9 1.0 C13 A:9ND501 2.4 24.8 1.0 F19 A:9ND501 2.7 30.3 1.0 CG2 A:ILE339 3.3 27.4 1.0 CD1 A:ILE277 3.4 40.9 1.0 C4 A:9ND501 3.6 21.1 1.0 CG2 A:ILE273 3.6 40.5 1.0 C9 A:9ND501 3.6 20.9 1.0 CG2 A:THR274 3.7 31.6 1.0 C5 A:9ND501 4.1 21.6 1.0 CD1 A:LEU352 4.1 35.7 1.0 CB A:ILE339 4.3 26.6 1.0 CD2 A:LEU352 4.4 37.4 1.0 CD1 A:ILE356 4.5 26.1 1.0 CB A:ILE273 4.5 40.9 1.0 N A:THR274 4.6 34.6 1.0 CA A:THR274 4.7 35.2 1.0 CG A:LEU352 4.7 36.0 1.0 C A:ILE273 4.8 38.8 1.0 CB A:THR274 4.8 39.2 1.0 CG1 A:ILE277 4.8 34.4 1.0 N1 A:9ND501 4.9 23.1 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:32.0 occ:1.00 F19 C:9ND501 0.0 32.0 1.0 C13 C:9ND501 1.3 27.8 1.0 C11 C:9ND501 2.3 28.0 1.0 C9 C:9ND501 2.4 25.1 1.0 F18 C:9ND501 2.7 30.3 1.0 CA C:PHE340 3.2 35.1 1.0 N C:PHE340 3.3 32.8 1.0 CB C:PHE340 3.3 37.2 1.0 CD1 C:PHE340 3.5 46.1 1.0 CD2 C:LEU352 3.6 38.7 1.0 C8 C:9ND501 3.6 26.2 1.0 C5 C:9ND501 3.6 25.6 1.0 CG2 C:ILE339 3.7 32.7 1.0 O C:SER336 3.8 31.0 1.0 CG C:PHE340 3.9 41.3 1.0 C C:ILE339 3.9 35.4 1.0 CD1 C:ILE356 4.0 34.0 1.0 C4 C:9ND501 4.1 26.8 1.0 CB C:ILE339 4.2 32.0 1.0 O C:ILE339 4.3 37.1 1.0 CG C:LEU352 4.4 37.1 1.0 C C:PHE340 4.6 40.1 1.0 CA C:ILE339 4.7 29.2 1.0 CD1 C:LEU352 4.7 37.4 1.0 CG2 C:THR274 4.7 46.2 1.0 CE1 C:PHE340 4.7 48.5 1.0 N3 C:9ND501 4.9 28.2 1.0 C C:SER336 4.9 29.0 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:30.3 occ:1.00 F18 C:9ND501 0.0 30.3 1.0 C11 C:9ND501 1.3 28.0 1.0 C13 C:9ND501 2.3 27.8 1.0 C8 C:9ND501 2.3 26.2 1.0 F19 C:9ND501 2.7 32.0 1.0 CG2 C:ILE339 3.3 32.7 1.0 CD1 C:ILE277 3.4 43.1 1.0 C4 C:9ND501 3.6 26.8 1.0 CG2 C:ILE273 3.6 40.1 1.0 C9 C:9ND501 3.6 25.1 1.0 CG2 C:THR274 3.7 46.2 1.0 CD1 C:LEU352 4.1 37.4 1.0 C5 C:9ND501 4.1 25.6 1.0 CD2 C:LEU352 4.4 38.7 1.0 CB C:ILE339 4.4 32.0 1.0 CD1 C:ILE356 4.4 34.0 1.0 CB C:ILE273 4.5 42.2 1.0 N C:THR274 4.6 40.4 1.0 CG C:LEU352 4.6 37.1 1.0 CA C:THR274 4.6 40.2 1.0 C C:ILE273 4.7 45.8 1.0 CB C:THR274 4.8 47.2 1.0 CG1 C:ILE277 4.8 39.9 1.0 N1 C:9ND501 4.9 29.2 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