Fluorine 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:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine 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 Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Ppargamma Ligand Binding Domain in Complex with Dibenzooxepine Derivative Compound-17, PDB code: 6k0t:
Jump to Fluorine binding site number: 1; 2;

Fluorine 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 Fluorine with other atoms in the F 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:F501 b:50.3 occ:1.00 F1 A:CTU501 0.0 50.3 1.0 C28 A:CTU501 1.3 46.6 1.0 C27 A:CTU501 2.3 46.5 1.0 C26 A:CTU501 2.4 44.6 1.0 CE A:MET463 2.9 70.2 1.0 CG2 A:ILE456 3.3 66.1 1.0 CZ A:PHE360 3.4 52.4 1.0 CB A:ILE456 3.5 63.7 1.0 CG1 A:ILE456 3.6 62.6 1.0 C23 A:CTU501 3.6 44.0 1.0 C22 A:CTU501 3.6 41.7 1.0 CE1 A:PHE360 3.7 49.7 1.0 SD A:MET463 3.9 69.6 1.0 C20 A:CTU501 4.1 41.8 1.0 CG1 A:ILE279 4.4 57.3 1.0 CD2 A:LEU453 4.6 51.6 1.0 CE2 A:PHE360 4.6 55.0 1.0 O1 A:CTU501 4.7 39.8 1.0 CD1 A:ILE456 4.7 65.5 1.0 CG2 A:ILE279 4.7 55.7 1.0 CB A:ILE279 4.9 56.9 1.0 CA A:ILE279 4.9 54.9 1.0 CB A:PHE282 5.0 41.2 1.0 CA A:ILE456 5.0 65.3 1.0

Fluorine 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 Fluorine with other atoms in the F 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:F501 b:48.2 occ:1.00 F1 C:CTU501 0.0 48.2 1.0 C28 C:CTU501 1.3 46.0 1.0 C27 C:CTU501 2.3 45.5 1.0 C26 C:CTU501 2.3 44.0 1.0 CG2 C:ILE456 3.1 62.5 1.0 CZ C:PHE360 3.4 55.1 1.0 CB C:ILE456 3.4 60.7 1.0 SD C:MET463 3.5 66.0 1.0 C23 C:CTU501 3.6 43.1 1.0 C22 C:CTU501 3.6 41.4 1.0 CG1 C:ILE456 3.6 59.5 1.0 CE1 C:PHE360 3.7 52.7 1.0 CE C:MET463 3.7 64.1 1.0 C20 C:CTU501 4.1 41.1 1.0 CD1 C:LEU453 4.5 47.9 1.0 CG2 C:ILE279 4.6 57.2 1.0 O1 C:CTU501 4.6 39.8 1.0 CE2 C:PHE360 4.6 58.0 1.0 CG1 C:ILE279 4.7 59.8 1.0 CD1 C:ILE456 4.7 62.8 1.0 CA C:ILE279 4.9 56.2 1.0 CA C:ILE456 4.9 63.2 1.0 CB C:ILE279 4.9 58.6 1.0 CB C:PHE282 5.0 41.9 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