Chlorine in PDB 5q0w: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q0w 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)	18.35 / 1.90
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	93.641, 93.641, 48.144, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 25.4

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

Bromine

(Br)

1 atom

The binding sites of Chlorine atom in the Ligand Binding to Farnesoid-X-Receptor (pdb code 5q0w). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q0w:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 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:63.8 occ:0.50 CL29 A:9LV501 0.0 63.8 0.5 C30 A:9LV501 1.4 62.6 0.5 C18 A:9LV501 1.7 62.4 0.5 C35 A:9LV501 2.2 63.6 0.5 C7 A:9LV501 2.6 61.5 0.5 C34 A:9LV501 2.7 62.7 0.5 C7 A:9LV501 2.7 60.3 0.5 O13 A:9LV501 2.8 57.5 0.5 O13 A:9LV501 2.8 58.2 0.5 S1 A:9LV501 3.3 58.3 0.5 S1 A:9LV501 3.3 57.6 0.5 CZ A:PHE333 3.3 31.7 1.0 CE A:MET454 3.4 62.8 1.0 C36 A:9LV501 3.5 64.1 0.5 C20 A:9LV501 3.6 51.5 1.0 C18 A:9LV501 3.8 63.6 0.5 CE1 A:PHE333 3.9 33.3 1.0 CE A:MET332 3.9 32.6 1.0 N8 A:9LV501 4.0 54.0 0.5 C36 A:9LV501 4.0 62.4 0.5 N8 A:9LV501 4.0 53.8 0.5 C30 A:9LV501 4.0 61.0 0.5 C34 A:9LV501 4.2 64.0 0.5 CE A:MET369 4.2 38.4 1.0 SD A:MET454 4.2 66.3 1.0 CE2 A:PHE333 4.2 32.9 1.0 ND1 A:HIS451 4.2 39.4 1.0 C35 A:9LV501 4.5 61.8 0.5 O12 A:9LV501 4.6 59.5 0.5 O12 A:9LV501 4.6 58.8 0.5 CE1 A:HIS451 4.9 38.5 1.0 C10 A:9LV501 4.9 47.7 1.0

Chlorine binding site 2 out of 2 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:65.3 occ:0.50 CL29 A:9LV501 0.0 65.3 0.5 C30 A:9LV501 1.4 61.0 0.5 C18 A:9LV501 1.7 63.6 0.5 C35 A:9LV501 2.1 61.8 0.5 C7 A:9LV501 2.6 60.3 0.5 C34 A:9LV501 2.7 64.0 0.5 C7 A:9LV501 2.7 61.5 0.5 O12 A:9LV501 2.9 59.5 0.5 O12 A:9LV501 2.9 58.8 0.5 O A:LEU291 3.3 21.0 1.0 S1 A:9LV501 3.3 57.6 0.5 S1 A:9LV501 3.3 58.3 0.5 C A:LEU291 3.3 22.5 1.0 C36 A:9LV501 3.5 62.4 0.5 CB A:LEU291 3.5 20.2 1.0 N A:THR292 3.6 19.3 1.0 C19 A:9LV501 3.6 51.7 1.0 C18 A:9LV501 3.8 62.4 0.5 N8 A:9LV501 3.9 54.0 0.5 N8 A:9LV501 3.9 53.8 0.5 CA A:THR292 3.9 19.6 1.0 C36 A:9LV501 4.0 64.1 0.5 CA A:LEU291 4.0 19.6 1.0 C30 A:9LV501 4.0 62.6 0.5 CB A:ALA295 4.1 21.7 1.0 C34 A:9LV501 4.1 62.7 0.5 OG1 A:THR292 4.4 33.6 1.0 C35 A:9LV501 4.5 63.6 0.5 O13 A:9LV501 4.6 57.5 0.5 O13 A:9LV501 4.7 58.2 0.5 CG A:LEU291 4.8 25.6 1.0 CE1 A:PHE288 4.8 35.0 1.0 CB A:THR292 4.8 26.3 1.0 O A:PHE288 4.9 30.2 1.0 C20 A:9LV501 4.9 51.5 1.0 CH2 A:TRP458 5.0 65.0 1.0 CD1 A:LEU291 5.0 26.4 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