Chlorine in PDB 6y3u: Crystal Structure of Ppargamma in Complex with Compound (R)-16

The structure of Crystal Structure of Ppargamma in Complex with Compound (R)-16, PDB code: 6y3u was solved by A.Chaikuad, T.Hanke, C.H.Arrowsmith, A.M.Edwards, C.Bountra, D.Merk, S.Knapp, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.88 / 2.62
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.059, 62.059, 167.021, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.4

The binding sites of Chlorine atom in the Crystal Structure of Ppargamma in Complex with Compound (R)-16 (pdb code 6y3u). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Ppargamma in Complex with Compound (R)-16, PDB code: 6y3u:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Ppargamma in Complex with Compound (R)-16


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Ppargamma in Complex with Compound (R)-16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:0.3 occ:1.00 CL1 A:MLQ501 0.0 0.3 1.0 C19 A:MLQ501 1.7 0.8 1.0 C20 A:MLQ501 2.7 0.2 1.0 C3 A:MLQ501 2.7 98.8 1.0 N A:MLQ501 3.1 80.6 1.0 S A:MLQ501 3.3 95.3 1.0 O A:MLQ501 3.5 1.0 1.0 CE1 A:HIS449 3.7 88.1 1.0 C4 A:MLQ501 3.8 77.8 1.0 C A:MLQ501 4.0 0.2 1.0 CB A:CYS285 4.0 83.5 1.0 C2 A:MLQ501 4.0 0.6 1.0 CD1 A:PHE363 4.1 92.8 1.0 NE2 A:HIS449 4.3 89.0 1.0 C18 A:MLQ501 4.5 75.2 1.0 C1 A:MLQ501 4.5 0.2 1.0 C5 A:MLQ501 4.5 87.0 1.0 CE1 A:PHE363 4.5 93.2 1.0 CG A:PHE363 4.6 88.9 1.0 O3 A:MLQ501 4.6 97.0 1.0 CE2 A:PHE282 4.7 0.9 1.0 CD2 A:PHE282 4.7 0.5 1.0 OE1 A:GLN286 4.8 1.0 1.0 ND1 A:HIS449 4.8 85.7 1.0 OH A:TYR327 4.8 0.1 1.0 SG A:CYS285 4.9 83.0 1.0 CB A:PHE363 4.9 81.7 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Ppargamma in Complex with Compound (R)-16


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Ppargamma in Complex with Compound (R)-16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:1.0 occ:1.00 CL A:MLQ501 0.0 1.0 1.0 C A:MLQ501 1.7 0.2 1.0 C20 A:MLQ501 2.7 0.2 1.0 C1 A:MLQ501 2.7 0.2 1.0 CA A:PHE282 3.6 88.5 1.0 CB A:PHE282 3.8 94.1 1.0 N A:PHE282 3.8 87.8 1.0 C19 A:MLQ501 4.0 0.8 1.0 C2 A:MLQ501 4.0 0.6 1.0 CG2 A:ILE281 4.0 88.5 1.0 CD1 A:LEU356 4.1 89.5 1.0 O A:PHE360 4.1 87.8 1.0 O A:ALA278 4.1 91.1 1.0 CB A:PHE360 4.3 93.0 1.0 C A:ILE281 4.3 89.2 1.0 CD1 A:PHE360 4.4 99.6 1.0 CD2 A:PHE282 4.5 0.5 1.0 CD2 A:PHE363 4.5 91.9 1.0 C3 A:MLQ501 4.5 98.8 1.0 CB A:ILE281 4.6 86.1 1.0 CG A:PHE282 4.6 0.9 1.0 O A:ILE281 4.7 89.3 1.0 CA A:PHE360 4.8 91.6 1.0 CG A:PHE360 4.8 0.1 1.0 CB A:PHE363 4.8 81.7 1.0 CG A:PHE363 4.8 88.9 1.0 C A:PHE360 4.8 90.4 1.0 SG A:CYS285 4.9 83.0 1.0

T.Hanke, S.Y.Cheung, W.Kilu, J.Heering, X.Ni, V.Planz, S.Schierle, G.Faudone, M.Friedrich, M.Wanior, O.Werz, M.Windbergs, E.Proschak, M.Schubert-Zsilavecz, A.Chaikuad, S.Knapp, D.Merk. A Selective Modulator of Peroxisome Proliferator-Activated Receptor Gamma with Unprecedented Binding Mode. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32267688
DOI: 10.1021/ACS.JMEDCHEM.9B01786