Chlorine in PDB 5q1d: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q1d 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)	27.67 / 1.89
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.440, 84.530, 190.540, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24.4

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 5q1d). 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: 5q1d:
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:40.8 occ:1.00 CL24 A:9ND501 0.0 40.8 1.0 C21 A:9ND501 1.7 33.5 1.0 C23 A:9ND501 2.7 30.4 1.0 C22 A:9ND501 2.7 33.8 1.0 SD A:MET454 3.7 53.8 1.0 CE1 A:HIS451 3.8 33.1 0.3 CZ A:PHE333 3.9 30.7 1.0 C16 A:9ND501 4.0 28.2 1.0 C17 A:9ND501 4.0 32.0 1.0 CD2 A:LEU291 4.1 33.9 1.0 ND1 A:HIS451 4.2 34.9 0.3 CD2 A:LEU455 4.2 42.2 1.0 CE1 A:PHE333 4.3 30.8 1.0 CD1 A:LEU291 4.4 28.4 1.0 CE A:MET332 4.4 34.6 1.0 CG A:MET454 4.4 50.4 1.0 C12 A:9ND501 4.5 27.5 1.0 CZ3 A:TRP458 4.7 32.7 1.0 CE2 A:PHE333 4.8 32.3 1.0 CD1 A:ILE361 4.8 48.3 1.0 CG A:LEU455 4.9 39.3 1.0 CG A:LEU291 4.9 29.0 1.0 NE2 A:HIS451 4.9 33.4 0.3

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 C:Cl501 b:45.5 occ:1.00 CL24 C:9ND501 0.0 45.5 1.0 C21 C:9ND501 1.7 40.2 1.0 C23 C:9ND501 2.7 36.7 1.0 C22 C:9ND501 2.7 40.0 1.0 CZ C:PHE333 3.7 39.1 1.0 SD C:MET454 3.9 56.7 1.0 CE1 C:HIS451 3.9 43.2 0.3 C16 C:9ND501 4.0 35.6 1.0 C17 C:9ND501 4.0 38.6 1.0 CE1 C:PHE333 4.1 40.2 1.0 ND1 C:HIS451 4.3 44.0 0.3 CD2 C:LEU291 4.3 37.2 1.0 CE C:MET332 4.4 40.3 1.0 CG C:MET454 4.5 52.1 1.0 CD2 C:LEU455 4.5 43.4 1.0 C12 C:9ND501 4.5 33.5 1.0 CD1 C:LEU291 4.5 32.5 1.0 CD1 C:ILE361 4.6 46.8 1.0 CE2 C:PHE333 4.7 40.9 1.0 CZ3 C:TRP458 4.7 37.0 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