Fluorine in PDB 5q0z: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q0z 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)	18.37 / 2.26
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.520, 83.550, 188.910, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 25.8

The binding sites of Fluorine atom in the Ligand Binding to Farnesoid-X-Receptor (pdb code 5q0z). 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: 5q0z:
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:F500 b:58.9 occ:1.00 F23 A:9M1500 0.0 58.9 1.0 C17 A:9M1500 1.4 58.6 1.0 C15 A:9M1500 2.4 58.7 1.0 C20 A:9M1500 2.4 58.4 1.0 F21 A:9M1500 2.7 59.2 1.0 CG2 A:ILE273 3.3 59.7 1.0 CG2 A:ILE339 3.4 58.7 1.0 C19 A:9M1500 3.6 58.3 1.0 C14 A:9M1500 3.6 59.0 1.0 CG2 A:THR274 3.7 69.2 1.0 CD1 A:ILE277 3.7 81.8 1.0 CD2 A:LEU352 3.8 63.1 1.0 CD1 A:LEU352 3.9 61.9 1.0 C13 A:9M1500 4.1 58.3 1.0 CB A:ILE339 4.2 55.3 1.0 CG A:LEU352 4.3 62.6 1.0 N A:THR274 4.5 63.1 1.0 CA A:THR274 4.6 65.3 1.0 CB A:ILE273 4.6 59.3 1.0 C A:ILE273 4.7 65.2 1.0 CD1 A:ILE356 4.7 68.8 1.0 CB A:THR274 4.7 72.4 1.0 O A:ILE273 4.8 65.7 1.0 CD1 A:ILE339 5.0 58.8 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:F500 b:59.2 occ:1.00 F21 A:9M1500 0.0 59.2 1.0 C15 A:9M1500 1.4 58.7 1.0 C17 A:9M1500 2.4 58.6 1.0 C14 A:9M1500 2.4 59.0 1.0 F23 A:9M1500 2.7 58.9 1.0 N A:PHE340 3.2 57.5 1.0 CB A:PHE340 3.3 61.4 1.0 CA A:PHE340 3.4 59.6 1.0 O A:SER336 3.4 51.3 1.0 C20 A:9M1500 3.6 58.4 1.0 C13 A:9M1500 3.6 58.3 1.0 CD2 A:LEU352 3.6 63.1 1.0 C A:ILE339 3.9 60.2 1.0 CG2 A:ILE339 3.9 58.7 1.0 CB A:ILE339 4.0 55.3 1.0 C19 A:9M1500 4.1 58.3 1.0 CD1 A:ILE356 4.2 68.8 1.0 CD1 A:PHE340 4.2 69.9 1.0 CG A:PHE340 4.2 65.3 1.0 C A:SER336 4.5 50.1 1.0 CG A:LEU352 4.5 62.6 1.0 CA A:ILE339 4.6 52.6 1.0 O A:ILE339 4.6 62.6 1.0 C8 A:9M1500 4.8 57.5 1.0 CA A:SER336 4.9 45.9 1.0 C A:PHE340 4.9 65.0 1.0 CD1 A:LEU352 4.9 61.9 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:F500 b:91.4 occ:1.00 F23 C:9M1500 0.0 91.4 1.0 C17 C:9M1500 1.4 89.2 1.0 C15 C:9M1500 2.4 86.8 1.0 C20 C:9M1500 2.4 90.1 1.0 F21 C:9M1500 2.7 87.2 1.0 CG2 C:ILE339 3.4 86.1 1.0 CG2 C:ILE273 3.6 1.0 1.0 C19 C:9M1500 3.6 88.1 1.0 C14 C:9M1500 3.6 85.0 1.0 CD2 C:LEU352 3.8 0.7 1.0 CD1 C:ILE277 3.8 0.5 1.0 CD1 C:LEU352 3.9 0.4 1.0 C13 C:9M1500 4.1 85.0 1.0 CG2 C:THR274 4.1 0.0 1.0 CD1 C:ILE356 4.2 0.9 1.0 CG C:LEU352 4.2 0.2 1.0 CB C:ILE339 4.4 82.3 1.0 CB C:ILE273 4.9 0.6 1.0 CE C:MET294 5.0 95.5 1.0 N C:THR274 5.0 0.2 1.0 CA C:THR274 5.0 0.2 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:F500 b:87.2 occ:1.00 F21 C:9M1500 0.0 87.2 1.0 C15 C:9M1500 1.4 86.8 1.0 C17 C:9M1500 2.3 89.2 1.0 C14 C:9M1500 2.4 85.0 1.0 F23 C:9M1500 2.7 91.4 1.0 O C:SER336 2.9 73.2 1.0 N C:PHE340 3.2 83.7 1.0 CB C:PHE340 3.2 87.5 1.0 CA C:PHE340 3.4 86.5 1.0 C20 C:9M1500 3.6 90.1 1.0 C13 C:9M1500 3.6 85.0 1.0 CG2 C:ILE339 3.7 86.1 1.0 CB C:ILE339 3.9 82.3 1.0 C C:ILE339 3.9 86.7 1.0 C C:SER336 3.9 71.4 1.0 C19 C:9M1500 4.1 88.1 1.0 CD2 C:LEU352 4.2 0.7 1.0 CG C:PHE340 4.3 91.8 1.0 CA C:SER336 4.3 66.6 1.0 CD1 C:PHE340 4.4 98.0 1.0 CA C:ILE339 4.4 79.3 1.0 CD1 C:ILE356 4.5 0.9 1.0 CB C:SER336 4.7 70.0 1.0 O C:ILE339 4.7 88.9 1.0 C8 C:9M1500 4.9 82.5 1.0 CE2 C:TYR373 4.9 86.9 1.0 C C:PHE340 5.0 93.3 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