Chlorine in PDB 3s9s: Ligand Binding Domain of Ppargamma Complexed with A Benzimidazole Partial Agonist

The structure of Ligand Binding Domain of Ppargamma Complexed with A Benzimidazole Partial Agonist, PDB code: 3s9s was solved by M.H.Lambert, R.X.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.30 / 2.55
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	56.086, 88.754, 122.605, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 28.4

The binding sites of Chlorine atom in the Ligand Binding Domain of Ppargamma Complexed with A Benzimidazole Partial Agonist (pdb code 3s9s). 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 Domain of Ppargamma Complexed with A Benzimidazole Partial Agonist, PDB code: 3s9s:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Ligand Binding Domain of Ppargamma Complexed with A Benzimidazole Partial Agonist


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ligand Binding Domain of Ppargamma Complexed with A Benzimidazole Partial Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1 b:51.1 occ:0.50 CL1 A:M0T1 0.0 51.1 0.5 CL1 A:M0T1 0.8 49.7 0.5 C13 A:M0T1 1.7 48.9 0.5 C13 A:M0T1 1.9 48.7 0.5 C14 A:M0T1 2.4 48.7 0.5 CL2 A:M0T1 2.4 50.3 0.5 C14 A:M0T1 2.7 48.8 0.5 C12 A:M0T1 2.7 48.1 0.5 CL2 A:M0T1 3.0 48.8 0.5 C12 A:M0T1 3.1 48.6 0.5 CG2 A:ILE281 3.6 55.6 1.0 C15 A:M0T1 3.8 47.9 0.5 CE A:MET348 3.9 49.0 1.0 C11 A:M0T1 4.0 47.4 0.5 O A:ILE281 4.0 55.6 1.0 C15 A:M0T1 4.0 47.6 0.5 CA A:ILE281 4.1 57.0 1.0 SG A:CYS285 4.2 52.6 1.0 C11 A:M0T1 4.3 47.2 0.5 SD A:MET348 4.3 46.9 1.0 CB A:ILE281 4.3 57.4 1.0 CD1 A:ILE262 4.4 68.0 1.0 C10 A:M0T1 4.5 47.3 0.5 C A:ILE281 4.5 56.7 1.0 C10 A:M0T1 4.5 47.4 0.5 CG2 A:ILE341 4.5 47.6 1.0 CG2 A:ILE262 4.6 67.6 1.0 CG1 A:ILE262 4.6 67.6 1.0 CG1 A:ILE281 4.7 57.2 1.0 N A:CYS285 4.7 51.6 1.0 CA A:GLY284 4.9 52.9 1.0 CD1 A:ILE341 4.9 50.9 1.0 C A:GLY284 5.0 52.1 1.0

Chlorine binding site 2 out of 4 in the Ligand Binding Domain of Ppargamma Complexed with A Benzimidazole Partial Agonist


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ligand Binding Domain of Ppargamma Complexed with A Benzimidazole Partial Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1 b:49.7 occ:0.50 CL1 A:M0T1 0.0 49.7 0.5 CL1 A:M0T1 0.8 51.1 0.5 C13 A:M0T1 1.7 48.7 0.5 C13 A:M0T1 1.8 48.9 0.5 CL2 A:M0T1 2.3 48.8 0.5 C14 A:M0T1 2.3 48.8 0.5 C12 A:M0T1 2.7 48.6 0.5 C14 A:M0T1 2.7 48.7 0.5 C12 A:M0T1 3.0 48.1 0.5 CL2 A:M0T1 3.1 50.3 0.5 C15 A:M0T1 3.7 47.6 0.5 C11 A:M0T1 3.9 47.2 0.5 C15 A:M0T1 3.9 47.9 0.5 CG2 A:ILE262 4.0 67.6 1.0 O A:ILE281 4.1 55.6 1.0 C11 A:M0T1 4.2 47.4 0.5 CD1 A:ILE262 4.2 68.0 1.0 CG2 A:ILE281 4.3 55.6 1.0 CG1 A:ILE262 4.3 67.6 1.0 SG A:CYS285 4.3 52.6 1.0 N A:CYS285 4.4 51.6 1.0 CA A:GLY284 4.4 52.9 1.0 C10 A:M0T1 4.4 47.4 0.5 C10 A:M0T1 4.4 47.3 0.5 CG2 A:ILE341 4.5 47.6 1.0 CE A:MET348 4.5 49.0 1.0 C A:GLY284 4.5 52.1 1.0 CA A:ILE281 4.5 57.0 1.0 CB A:ILE262 4.7 68.4 1.0 CD1 A:ILE341 4.8 50.9 1.0 C A:ILE281 4.8 56.7 1.0 CB A:ILE341 4.8 48.8 1.0 CB A:ILE281 4.9 57.4 1.0

Chlorine binding site 3 out of 4 in the Ligand Binding Domain of Ppargamma Complexed with A Benzimidazole Partial Agonist


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ligand Binding Domain of Ppargamma Complexed with A Benzimidazole Partial Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1 b:48.8 occ:0.50 CL2 A:M0T1 0.0 48.8 0.5 C12 A:M0T1 1.5 48.6 0.5 C14 A:M0T1 1.7 48.8 0.5 C13 A:M0T1 2.1 48.7 0.5 CL1 A:M0T1 2.3 49.7 0.5 C13 A:M0T1 2.7 48.9 0.5 C15 A:M0T1 2.7 47.6 0.5 C11 A:M0T1 2.7 47.2 0.5 CL1 A:M0T1 3.0 51.1 0.5 C14 A:M0T1 3.4 48.7 0.5 O A:HOH22 3.4 4.0 1.0 C A:GLY284 3.6 52.1 1.0 O A:GLY284 3.8 52.4 1.0 C10 A:M0T1 3.8 47.4 0.5 N A:CYS285 3.9 51.6 1.0 C12 A:M0T1 3.9 48.1 0.5 C10 A:M0T1 4.0 47.3 0.5 CA A:GLY284 4.0 52.9 1.0 CG2 A:ILE262 4.1 67.6 1.0 C15 A:M0T1 4.1 47.9 0.5 CA A:CYS285 4.3 50.9 1.0 C11 A:M0T1 4.4 47.4 0.5 CB A:ILE341 4.6 48.8 1.0 CG2 A:ILE341 4.6 47.6 1.0 CL2 A:M0T1 4.7 50.3 0.5 SG A:CYS285 4.7 52.6 1.0 CB A:ARG288 4.9 47.9 1.0

Chlorine binding site 4 out of 4 in the Ligand Binding Domain of Ppargamma Complexed with A Benzimidazole Partial Agonist


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ligand Binding Domain of Ppargamma Complexed with A Benzimidazole Partial Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1 b:50.3 occ:0.50 CL2 A:M0T1 0.0 50.3 0.5 C12 A:M0T1 1.4 48.1 0.5 C14 A:M0T1 1.7 48.7 0.5 C13 A:M0T1 2.1 48.9 0.5 CL1 A:M0T1 2.4 51.1 0.5 C11 A:M0T1 2.7 47.4 0.5 C15 A:M0T1 2.7 47.9 0.5 C13 A:M0T1 2.7 48.7 0.5 CL1 A:M0T1 3.1 49.7 0.5 SD A:MET348 3.1 46.9 1.0 C14 A:M0T1 3.4 48.8 0.5 CG2 A:ILE281 3.4 55.6 1.0 C10 A:M0T1 3.8 47.3 0.5 CE A:MET348 3.8 49.0 1.0 C10 A:M0T1 3.9 47.4 0.5 CD2 A:LEU353 3.9 46.6 1.0 C12 A:M0T1 4.0 48.6 0.5 SG A:CYS285 4.1 52.6 1.0 C15 A:M0T1 4.1 47.6 0.5 CG2 A:ILE341 4.2 47.6 1.0 CG A:MET348 4.4 47.2 1.0 CB A:MET348 4.4 45.4 1.0 C11 A:M0T1 4.5 47.2 0.5 CD1 A:LEU353 4.6 46.1 1.0 CL2 A:M0T1 4.7 48.8 0.5 CG A:LEU353 4.8 49.1 1.0 CB A:ILE281 4.8 57.4 1.0 CG1 A:VAL339 4.9 46.6 1.0

M.Sime, A.C.Allan, P.Chapman, C.Fieldhouse, G.M.Giblin, M.P.Healy, M.H.Lambert, L.M.Leesnitzer, A.Lewis, R.V.Merrihew, R.A.Rutter, R.Sasse, B.G.Shearer, T.M.Wilson, R.X.Xu, D.J.Virley. Discovery of GSK1997132B A Novel Centrally Penetrant Benzimidazole Ppargamma Partial Agonist. Bioorg.Med.Chem.Lett. V. 21 5568 2011.
ISSN: ISSN 0960-894X
PubMed: 21798739
DOI: 10.1016/J.BMCL.2011.06.088