Chlorine in PDB 5q0n: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q0n 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)	41.27 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.340, 84.530, 191.100, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.6

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

Fluorine

(F)

4 atoms

The binding sites of Chlorine atom in the Ligand Binding to Farnesoid-X-Receptor (pdb code 5q0n). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q0n:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Ligand Binding to Farnesoid-X-Receptor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ligand Binding to Farnesoid-X-Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:38.6 occ:1.00 CL33 A:9L4501 0.0 38.6 1.0 C30 A:9L4501 1.7 32.8 1.0 C31 A:9L4501 2.7 29.3 1.0 C32 A:9L4501 2.7 30.5 1.0 CE A:MET454 3.9 51.3 1.0 CZ A:PHE333 3.9 33.6 1.0 C25 A:9L4501 4.0 28.8 1.0 C24 A:9L4501 4.0 30.2 1.0 SD A:MET454 4.1 54.8 1.0 CD2 A:LEU455 4.1 48.8 1.0 CG A:MET454 4.2 51.8 1.0 CD2 A:LEU291 4.3 38.4 1.0 CE1 A:PHE333 4.4 33.8 1.0 CZ3 A:TRP458 4.4 41.5 1.0 C14 A:9L4501 4.5 30.0 1.0 CD1 A:LEU291 4.6 32.9 1.0 CG A:LEU455 4.6 48.1 1.0 CB A:MET454 4.9 48.5 1.0 CE2 A:PHE333 4.9 34.5 1.0

Chlorine binding site 2 out of 4 in the Ligand Binding to Farnesoid-X-Receptor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ligand Binding to Farnesoid-X-Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:39.3 occ:1.00 CL28 A:9L4501 0.0 39.3 1.0 C17 A:9L4501 1.7 35.4 1.0 C18 A:9L4501 2.7 32.7 1.0 C12 A:9L4501 2.7 33.9 1.0 N9 A:9L4501 3.0 32.4 1.0 C6 A:9L4501 3.4 31.5 1.0 O19 A:9L4501 3.6 33.9 1.0 CG A:MET332 3.6 40.5 1.0 N A:ALA295 3.7 29.2 1.0 CB A:MET294 3.7 33.2 1.0 SD A:MET332 3.8 48.6 1.0 CA A:ALA295 3.9 28.2 1.0 C A:MET294 3.9 32.8 1.0 C16 A:9L4501 4.0 31.3 1.0 C21 A:9L4501 4.0 33.2 1.0 CB A:ALA295 4.2 28.5 1.0 O A:MET294 4.2 31.6 1.0 CD1 A:LEU291 4.4 32.9 1.0 CA A:MET294 4.5 30.6 1.0 C7 A:9L4501 4.5 31.3 1.0 C22 A:9L4501 4.5 31.9 1.0 O A:LEU291 4.5 35.7 1.0 CE A:MET294 4.7 41.3 1.0 OG A:SER336 4.8 28.6 1.0 CG A:MET294 4.9 38.9 1.0 C25 A:9L4501 4.9 28.8 1.0 CB A:MET332 4.9 33.6 1.0 CB A:HIS298 5.0 28.8 1.0

Chlorine binding site 3 out of 4 in the Ligand Binding to Farnesoid-X-Receptor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ligand Binding to Farnesoid-X-Receptor within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl501 b:48.7 occ:1.00 CL33 C:9L4501 0.0 48.7 1.0 C30 C:9L4501 1.7 42.6 1.0 C32 C:9L4501 2.7 41.7 1.0 C31 C:9L4501 2.7 37.3 1.0 CZ C:PHE333 3.7 42.6 1.0 C25 C:9L4501 4.0 35.7 1.0 C24 C:9L4501 4.0 39.6 1.0 CG C:MET454 4.1 72.2 1.0 CE1 C:PHE333 4.2 44.7 1.0 CD2 C:LEU455 4.3 69.2 1.0 CD2 C:LEU291 4.3 51.4 1.0 CZ3 C:TRP458 4.4 53.7 1.0 C14 C:9L4501 4.5 36.2 1.0 CD1 C:LEU291 4.5 45.8 1.0 SD C:MET454 4.6 74.9 1.0 CD1 C:ILE361 4.6 58.8 1.0 CE2 C:PHE333 4.8 43.9 1.0 CE C:MET454 4.8 70.6 1.0 CG C:LEU455 4.9 67.3 1.0 SD C:MET369 5.0 66.1 1.0 CE C:MET332 5.0 48.6 1.0

Chlorine binding site 4 out of 4 in the Ligand Binding to Farnesoid-X-Receptor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ligand Binding to Farnesoid-X-Receptor within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl501 b:35.1 occ:1.00 CL28 C:9L4501 0.0 35.1 1.0 C17 C:9L4501 1.7 34.7 1.0 C18 C:9L4501 2.7 34.6 1.0 C12 C:9L4501 2.7 39.8 1.0 N9 C:9L4501 3.0 42.8 1.0 C6 C:9L4501 3.5 44.0 1.0 CG C:MET332 3.5 46.0 1.0 CB C:MET294 3.7 52.5 1.0 N C:ALA295 3.8 45.1 1.0 SD C:MET332 3.8 52.4 1.0 O19 C:9L4501 3.8 44.0 1.0 C C:MET294 3.9 49.5 1.0 CA C:ALA295 4.0 43.4 1.0 C16 C:9L4501 4.0 37.4 1.0 C21 C:9L4501 4.0 40.2 1.0 O C:MET294 4.2 47.6 1.0 CB C:ALA295 4.3 43.8 1.0 CD1 C:LEU291 4.5 45.8 1.0 C7 C:9L4501 4.5 42.7 1.0 C22 C:9L4501 4.5 37.5 1.0 CA C:MET294 4.5 49.6 1.0 O C:LEU291 4.6 50.7 1.0 OG C:SER336 4.7 39.7 1.0 CB C:MET332 4.8 40.8 1.0 C25 C:9L4501 4.8 35.7 1.0 CG C:MET294 4.9 58.9 1.0 CB C:HIS298 5.0 35.6 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