Chlorine in PDB 6k0t: Crystal Structure of Ppargamma Ligand Binding Domain in Complex with Dibenzooxepine Derivative Compound-17

The structure of Crystal Structure of Ppargamma Ligand Binding Domain in Complex with Dibenzooxepine Derivative Compound-17, PDB code: 6k0t was solved by M.Suzuki, K.Yamamoto, Y.Takahashi, J.Saito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.84
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.340, 54.060, 70.490, 94.26, 103.94, 89.95
R / Rfree (%)	19.2 / 24.4

The structure of Crystal Structure of Ppargamma Ligand Binding Domain in Complex with Dibenzooxepine Derivative Compound-17 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Ppargamma Ligand Binding Domain in Complex with Dibenzooxepine Derivative Compound-17 (pdb code 6k0t). 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 Ligand Binding Domain in Complex with Dibenzooxepine Derivative Compound-17, PDB code: 6k0t:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Ppargamma Ligand Binding Domain in Complex with Dibenzooxepine Derivative Compound-17


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 Ligand Binding Domain in Complex with Dibenzooxepine Derivative Compound-17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:42.4 occ:1.00 CL1 A:CTU501 0.0 42.4 1.0 C10 A:CTU501 1.7 39.3 1.0 C5 A:CTU501 2.7 36.4 1.0 C14 A:CTU501 2.7 40.9 1.0 N2 A:CTU501 3.1 33.2 1.0 O A:HOH806 3.4 32.4 1.0 SD A:CME285 3.5 41.2 1.0 CG2 A:ILE341 3.7 43.6 1.0 CG2 A:VAL339 3.7 32.9 1.0 O A:HOH738 3.9 35.3 1.0 CG1 A:VAL339 4.0 36.8 1.0 N1 A:CTU501 4.0 36.7 1.0 CD1 A:LEU330 4.0 32.4 1.0 C11 A:CTU501 4.0 41.4 1.0 O A:HOH653 4.4 31.0 1.0 C2 A:CTU501 4.4 32.5 1.0 CZ A:CME285 4.5 44.9 1.0 CB A:VAL339 4.5 34.7 1.0 C6 A:CTU501 4.5 39.1 1.0 CE A:CME285 4.6 42.8 1.0 O A:LEU340 4.8 34.9 1.0 SG A:CME285 4.8 40.3 1.0 C1 A:CTU501 4.9 34.5 1.0 CB A:ILE341 4.9 44.1 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Ppargamma Ligand Binding Domain in Complex with Dibenzooxepine Derivative Compound-17


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 Ligand Binding Domain in Complex with Dibenzooxepine Derivative Compound-17 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl501 b:48.0 occ:1.00 CL1 C:CTU501 0.0 48.0 1.0 C10 C:CTU501 1.7 42.7 1.0 C5 C:CTU501 2.7 39.4 1.0 C14 C:CTU501 2.7 43.9 1.0 N2 C:CTU501 3.1 35.8 1.0 SD C:CME285 3.6 43.3 1.0 O C:HOH730 3.8 43.6 1.0 N1 C:CTU501 3.9 39.7 1.0 CG2 C:ILE341 4.0 46.4 1.0 CG1 C:VAL339 4.0 38.8 1.0 C11 C:CTU501 4.0 44.0 1.0 CD1 C:LEU330 4.1 32.9 1.0 CG2 C:VAL339 4.1 34.9 1.0 C2 C:CTU501 4.4 35.8 1.0 C6 C:CTU501 4.5 41.7 1.0 CB C:VAL339 4.7 37.0 1.0 CZ C:CME285 4.7 48.1 1.0 SG C:CME285 4.7 40.7 1.0 CE C:CME285 4.8 45.7 1.0 CE C:MET364 4.8 38.5 1.0 C1 C:CTU501 4.9 37.1 1.0

K.Yamamoto, T.Tamura, R.Nakamura, S.Hosoe, M.Matsubara, K.Nagata, H.Kodaira, T.Uemori, Y.Takahashi, M.Suzuki, J.I.Saito, K.Ueno, S.Shuto. Development of A Novel Class of Peroxisome Proliferator-Activated Receptor (Ppar) Gamma Ligands As An Anticancer Agent with A Unique Binding Mode Based on A Non-Thiazolidinedione Scaffold. Bioorg.Med.Chem. V. 27 15122 2019.
ISSN: ESSN 1464-3391
PubMed: 31623970
DOI: 10.1016/J.BMC.2019.115122