Fluorine in PDB 5q13: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q13 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)	35.53 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.035, 36.405, 95.533, 90.00, 99.42, 90.00
R / Rfree (%)	17.1 / 22.6

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

Chlorine

(Cl)

4 atoms

The binding sites of Fluorine atom in the Ligand Binding to Farnesoid-X-Receptor (pdb code 5q13). 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: 5q13:
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:16.8 occ:1.00 F32 A:9MD501 0.0 16.8 1.0 C1 A:9MD501 1.3 13.6 1.0 C4 A:9MD501 2.4 10.0 1.0 C2 A:9MD501 2.4 14.6 1.0 CL33 A:9MD501 2.9 20.0 1.0 CD2 A:LEU352 3.1 17.6 1.0 N A:PHE340 3.2 11.7 1.0 CA A:PHE340 3.2 12.7 1.0 O A:SER336 3.5 11.2 1.0 CB A:PHE340 3.5 14.3 1.0 C5 A:9MD501 3.6 11.8 1.0 C3 A:9MD501 3.6 10.4 1.0 C A:ILE339 3.8 14.1 1.0 CG2 A:ILE339 4.0 14.9 1.0 C6 A:9MD501 4.1 12.0 1.0 CB A:ILE339 4.1 13.1 1.0 CD2 A:PHE340 4.1 19.6 1.0 CD1 A:LEU352 4.2 16.5 1.0 CG A:LEU352 4.2 15.6 1.0 CG A:PHE340 4.3 17.3 1.0 O A:ILE339 4.3 14.3 1.0 CA A:ILE339 4.5 10.3 1.0 C A:SER336 4.5 11.6 1.0 C A:PHE340 4.6 16.5 1.0 CE1 A:HIS348 4.7 24.4 1.0 N9 A:9MD501 4.9 10.6 1.0 CA A:SER336 5.0 8.2 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:19.6 occ:1.00 F32 C:9MD501 0.0 19.6 1.0 C1 C:9MD501 1.4 13.6 1.0 C4 C:9MD501 2.4 9.1 1.0 C2 C:9MD501 2.4 13.9 1.0 CL33 C:9MD501 3.0 17.9 1.0 N C:PHE340 3.1 7.5 1.0 CA C:PHE340 3.2 8.1 1.0 CB C:PHE340 3.4 9.6 1.0 O C:SER336 3.4 8.2 1.0 C5 C:9MD501 3.6 8.9 1.0 C3 C:9MD501 3.6 11.3 1.0 C C:ILE339 3.6 10.2 1.0 CG2 C:ILE339 3.8 9.1 1.0 CD1 C:PHE340 3.8 15.1 1.0 CD1 C:ILE356 3.9 21.8 1.0 CD2 C:LEU352 4.0 16.2 1.0 CB C:ILE339 4.0 10.6 1.0 CG C:PHE340 4.1 11.8 1.0 C6 C:9MD501 4.1 10.9 1.0 O C:ILE339 4.2 9.3 1.0 CA C:ILE339 4.4 8.3 1.0 C C:SER336 4.5 9.3 1.0 CG C:LEU352 4.6 15.1 1.0 C C:PHE340 4.6 12.1 1.0 CD1 C:LEU352 4.8 15.9 1.0 N9 C:9MD501 4.9 10.2 1.0 CA C:SER336 5.0 6.5 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