Chlorine in PDB 5q13: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q13 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)	35.53 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.035, 36.405, 95.533, 90.00, 99.42, 90.00
R / Rfree (%)	17.1 / 22.6

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

Fluorine

(F)

2 atoms

The binding sites of Chlorine atom in the Ligand Binding to Farnesoid-X-Receptor (pdb code 5q13). 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: 5q13:
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:28.4 occ:1.00 CL34 A:9MD501 0.0 28.4 1.0 C29 A:9MD501 1.7 19.8 1.0 C28 A:9MD501 2.7 17.2 1.0 C31 A:9MD501 2.7 16.2 1.0 CE A:MET454 3.0 17.4 1.0 CZ A:PHE333 3.6 11.9 1.0 CD2 A:HIS451 3.7 16.9 1.0 CH2 A:TRP458 3.8 18.3 1.0 CE A:MET332 3.9 26.6 1.0 C27 A:9MD501 4.0 17.4 1.0 C30 A:9MD501 4.0 16.4 1.0 SD A:MET454 4.0 20.3 1.0 CE2 A:PHE333 4.2 11.9 1.0 CE1 A:PHE333 4.2 15.1 1.0 NE2 A:HIS451 4.4 17.3 1.0 CZ3 A:TRP458 4.4 17.9 1.0 C10 A:9MD501 4.5 15.4 1.0 SD A:MET332 4.7 30.7 1.0 CD2 A:LEU291 4.8 21.7 1.0 CZ2 A:TRP458 4.8 18.8 1.0 CG A:HIS451 4.8 14.8 1.0 CD1 A:LEU291 4.8 16.0 1.0 CE A:MET369 4.8 16.1 0.7

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:20.0 occ:1.00 CL33 A:9MD501 0.0 20.0 1.0 C2 A:9MD501 1.7 14.6 1.0 C3 A:9MD501 2.7 10.4 1.0 C1 A:9MD501 2.7 13.6 1.0 F32 A:9MD501 2.9 16.8 1.0 CG2 A:ILE339 3.6 14.9 1.0 CD1 A:ILE273 3.7 36.7 1.0 CD1 A:LEU352 3.9 16.5 1.0 CG1 A:ILE273 3.9 33.0 1.0 CG1 A:ILE277 3.9 20.1 1.0 C6 A:9MD501 3.9 12.0 1.0 C4 A:9MD501 4.0 10.0 1.0 CD1 A:ILE277 4.1 26.2 1.0 CE1 A:HIS348 4.3 24.4 1.0 CD2 A:LEU352 4.3 17.6 1.0 NE2 A:HIS348 4.4 24.8 1.0 CB A:ILE339 4.4 13.1 1.0 C5 A:9MD501 4.5 11.8 1.0 CG A:LEU352 4.6 15.6 1.0 CG2 A:ILE273 5.0 32.7 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:26.9 occ:1.00 CL34 C:9MD501 0.0 26.9 1.0 C29 C:9MD501 1.7 21.0 1.0 C28 C:9MD501 2.7 19.3 1.0 C31 C:9MD501 2.7 16.3 1.0 SD C:MET454 3.3 18.3 0.5 CD2 C:LEU455 3.6 17.0 1.0 CZ C:PHE333 3.8 10.8 1.0 CG C:MET454 3.9 15.1 0.5 C27 C:9MD501 4.0 15.2 1.0 C30 C:9MD501 4.0 12.8 1.0 CB C:MET454 4.4 13.4 0.5 CG C:LEU455 4.4 16.4 1.0 CE1 C:PHE333 4.4 12.3 1.0 CB C:MET454 4.4 12.7 0.5 CZ3 C:TRP458 4.5 14.4 1.0 C10 C:9MD501 4.5 11.8 1.0 CE2 C:PHE333 4.7 12.6 1.0 CE C:MET454 4.9 15.9 0.5 CE C:MET332 4.9 22.2 1.0 SD C:MET454 4.9 20.4 0.5 CG C:LEU291 4.9 13.1 1.0 CD2 C:LEU291 5.0 12.2 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:17.9 occ:1.00 CL33 C:9MD501 0.0 17.9 1.0 C2 C:9MD501 1.7 13.9 1.0 C3 C:9MD501 2.7 11.3 1.0 C1 C:9MD501 2.7 13.6 1.0 F32 C:9MD501 3.0 19.6 1.0 CG2 C:ILE339 3.5 9.1 1.0 CD1 C:ILE277 3.5 22.2 1.0 CG2 C:ILE273 3.6 15.1 1.0 CG2 C:THR274 3.7 17.7 1.0 CD1 C:LEU352 3.9 15.9 1.0 C6 C:9MD501 3.9 10.9 1.0 C4 C:9MD501 4.0 9.1 1.0 CD2 C:LEU352 4.4 16.2 1.0 CB C:ILE339 4.4 10.6 1.0 C5 C:9MD501 4.5 8.9 1.0 CG C:LEU352 4.6 15.1 1.0 N C:THR274 4.7 12.8 1.0 CB C:ILE273 4.7 16.1 1.0 CD1 C:ILE356 4.7 21.8 1.0 CA C:THR274 4.7 13.4 1.0 C C:ILE273 4.8 16.4 1.0 CB C:THR274 4.8 20.1 1.0 CG1 C:ILE277 4.8 15.4 1.0 O C:ILE273 4.9 14.8 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