Fluorine in PDB 5q12: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q12 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)	18.63 / 2.00
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	93.315, 93.315, 47.882, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 23.3

The binding sites of Fluorine atom in the Ligand Binding to Farnesoid-X-Receptor (pdb code 5q12). 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: 5q12:
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:30.1 occ:1.00 F24 A:9MA501 0.0 30.1 1.0 C21 A:9MA501 1.4 29.5 1.0 C20 A:9MA501 2.3 27.0 1.0 C27 A:9MA501 2.3 28.8 1.0 C1 A:9MA501 2.8 26.2 1.0 CB A:ALA295 3.3 20.1 1.0 C2 A:9MA501 3.3 25.9 1.0 CA A:ALA295 3.3 19.4 1.0 CE A:MET332 3.3 36.2 1.0 C19 A:9MA501 3.5 25.6 1.0 CD2 A:HIS298 3.5 29.2 1.0 N3 A:9MA501 3.5 23.8 1.0 C22 A:9MA501 3.6 28.3 1.0 C25 A:9MA501 3.6 28.6 1.0 N10 A:9MA501 3.7 27.3 1.0 N A:ALA295 4.0 20.2 1.0 C14 A:9MA501 4.0 25.0 1.0 C12 A:9MA501 4.0 24.5 1.0 C26 A:9MA501 4.1 28.0 1.0 CG A:HIS298 4.2 26.5 1.0 N6 A:9MA501 4.3 26.1 1.0 NE2 A:HIS298 4.4 29.1 1.0 C5 A:9MA501 4.5 28.2 1.0 CB A:HIS298 4.5 21.6 1.0 C A:ALA295 4.5 22.7 1.0 O A:ALA295 4.6 22.2 1.0 C A:MET294 4.7 22.7 1.0 F23 A:9MA501 4.7 29.7 1.0 CB A:MET332 4.7 27.7 1.0 O A:LEU291 4.8 23.7 1.0 O A:MET294 4.9 20.9 1.0 SD A:MET332 4.9 39.1 1.0 CG A:MET332 5.0 33.2 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 A:F501 b:29.7 occ:1.00 F23 A:9MA501 0.0 29.7 1.0 C22 A:9MA501 1.4 28.3 1.0 C26 A:9MA501 2.3 28.0 1.0 C20 A:9MA501 2.4 27.0 1.0 C1 A:9MA501 2.8 26.2 1.0 N10 A:9MA501 3.2 27.3 1.0 CD2 A:HIS451 3.3 25.4 1.0 CE A:MET454 3.5 31.0 0.5 C13 A:9MA501 3.5 24.4 1.0 C18 A:9MA501 3.5 23.8 1.0 C21 A:9MA501 3.6 29.5 1.0 NE2 A:HIS451 3.6 25.0 1.0 C25 A:9MA501 3.6 28.6 1.0 C2 A:9MA501 3.7 25.9 1.0 CZ A:PHE333 3.8 35.5 1.0 C17 A:9MA501 3.9 25.1 1.0 C12 A:9MA501 3.9 24.5 1.0 CE1 A:PHE333 4.0 36.1 1.0 CE A:MET454 4.0 38.0 0.5 C27 A:9MA501 4.1 28.8 1.0 C5 A:9MA501 4.2 28.2 1.0 CE A:MET369 4.3 39.2 1.0 N3 A:9MA501 4.3 23.8 1.0 SD A:MET454 4.4 41.1 0.5 N6 A:9MA501 4.5 26.1 1.0 C15 A:9MA501 4.6 25.9 1.0 CE2 A:PHE333 4.6 37.0 1.0 C14 A:9MA501 4.6 25.0 1.0 CG A:HIS451 4.6 25.3 1.0 F24 A:9MA501 4.7 30.1 1.0 SD A:MET454 4.7 35.6 0.5 CD1 A:PHE333 4.9 34.4 1.0 C16 A:9MA501 4.9 26.7 1.0 CE1 A:HIS451 4.9 25.5 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