Chlorine in PDB 5z5s: Crystal Structure of the Ppargamma-Lbd Complexed with Compound 13AB

The structure of Crystal Structure of the Ppargamma-Lbd Complexed with Compound 13AB, PDB code: 5z5s was solved by Y.Matsui, H.Hanzawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.408, 54.015, 66.242, 90.00, 106.48, 90.00
R / Rfree (%)	n/a / n/a

The structure of Crystal Structure of the Ppargamma-Lbd Complexed with Compound 13AB also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of the Ppargamma-Lbd Complexed with Compound 13AB (pdb code 5z5s). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of the Ppargamma-Lbd Complexed with Compound 13AB, PDB code: 5z5s:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of the Ppargamma-Lbd Complexed with Compound 13AB


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 the Ppargamma-Lbd Complexed with Compound 13AB within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:37.0 occ:0.50 CL1 A:RTE501 0.0 37.0 0.5 CL1 A:RTE501 0.7 34.6 0.5 C1 A:RTE501 1.7 33.2 0.5 C1 A:RTE501 1.9 31.5 0.5 F9 A:RTE501 2.5 32.2 0.5 C2 A:RTE501 2.5 31.8 0.5 C6 A:RTE501 2.7 33.4 0.5 C2 A:RTE501 2.7 33.1 0.5 F9 A:RTE501 2.9 33.4 0.5 C6 A:RTE501 3.0 30.8 0.5 N A:GLU259 3.3 37.0 1.0 C A:GLY258 3.4 35.8 1.0 CA A:GLU259 3.5 38.6 1.0 CD1 A:ILE249 3.5 27.2 1.0 O A:GLY258 3.6 36.0 1.0 O A:LEU255 3.9 27.5 1.0 C3 A:RTE501 3.9 30.8 0.5 C5 A:RTE501 4.0 32.2 0.5 C3 A:RTE501 4.0 32.0 0.5 CD1 A:ILE262 4.1 32.5 1.0 CB A:GLU259 4.1 40.3 1.0 CA A:GLY258 4.1 34.8 1.0 C5 A:RTE501 4.2 30.3 0.5 CD1 A:LEU255 4.2 30.8 1.0 C4 A:RTE501 4.5 31.1 0.5 C4 A:RTE501 4.6 29.7 0.5 CG1 A:ILE262 4.6 33.8 1.0 CB A:ILE262 4.7 33.6 1.0 C A:GLU259 4.8 38.9 1.0 CG A:GLU259 4.8 43.3 1.0 C A:LEU255 4.9 28.3 1.0 CG1 A:ILE249 4.9 26.4 1.0 CG A:LEU255 5.0 28.9 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of the Ppargamma-Lbd Complexed with Compound 13AB


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 the Ppargamma-Lbd Complexed with Compound 13AB within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:34.6 occ:0.50 CL1 A:RTE501 0.0 34.6 0.5 CL1 A:RTE501 0.7 37.0 0.5 C1 A:RTE501 1.7 31.5 0.5 C1 A:RTE501 1.8 33.2 0.5 C2 A:RTE501 2.5 33.1 0.5 F9 A:RTE501 2.6 33.4 0.5 C6 A:RTE501 2.7 30.8 0.5 C2 A:RTE501 2.7 31.8 0.5 C6 A:RTE501 2.9 33.4 0.5 F9 A:RTE501 2.9 32.2 0.5 N A:GLU259 3.2 37.0 1.0 O A:LEU255 3.4 27.5 1.0 CA A:GLU259 3.4 38.6 1.0 C A:GLY258 3.6 35.8 1.0 CD1 A:ILE249 3.7 27.2 1.0 CD1 A:LEU255 3.7 30.8 1.0 CB A:GLU259 3.8 40.3 1.0 C3 A:RTE501 3.8 32.0 0.5 C5 A:RTE501 4.0 30.3 0.5 O A:GLY258 4.0 36.0 1.0 C3 A:RTE501 4.0 30.8 0.5 C5 A:RTE501 4.1 32.2 0.5 CA A:GLY258 4.3 34.8 1.0 C A:LEU255 4.4 28.3 1.0 CG A:LEU255 4.4 28.9 1.0 C4 A:RTE501 4.5 31.1 0.5 C4 A:RTE501 4.5 29.7 0.5 CG A:GLU259 4.5 43.3 1.0 CA A:LEU255 4.6 27.5 1.0 CD1 A:ILE262 4.7 32.5 1.0 C A:GLU259 4.8 38.9 1.0 CG1 A:ILE249 4.9 26.4 1.0 N A:GLY258 5.0 33.2 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of the Ppargamma-Lbd Complexed with Compound 13AB


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Ppargamma-Lbd Complexed with Compound 13AB within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:13.3 occ:1.00 O A:HOH715 3.1 26.2 1.0 O A:HOH648 3.4 23.3 1.0 ND2 A:ASN375 3.5 16.1 1.0 NH2 A:ARG234 3.6 21.5 1.0 CA A:ASN335 3.7 23.4 1.0 CB A:ASN375 3.8 14.5 1.0 O A:MET334 3.9 19.5 1.0 CG A:ASN375 4.1 15.4 1.0 CB A:ASN335 4.3 24.3 1.0 N A:LYS336 4.3 25.3 1.0 C A:ASN335 4.4 23.2 1.0 CA A:VAL372 4.5 17.5 1.0 C A:MET334 4.7 19.3 1.0 N A:ASN335 4.7 21.8 1.0 CZ A:ARG234 4.7 21.0 1.0 O A:HOH852 4.8 36.0 1.0 O A:VAL372 4.8 17.7 1.0 O A:ALA371 4.9 15.1 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of the Ppargamma-Lbd Complexed with Compound 13AB


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Ppargamma-Lbd Complexed with Compound 13AB within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:14.7 occ:1.00 O A:HOH697 3.2 35.5 1.0 NH1 A:ARG397 3.5 11.6 1.0 CD A:PRO398 3.7 14.5 1.0 CD A:ARG397 3.8 13.6 1.0 O A:HOH752 3.8 30.0 1.0 CB A:TYR320 4.3 15.8 1.0 CG A:PRO398 4.4 17.1 1.0 CA A:ARG397 4.4 12.8 1.0 CD1 A:TYR320 4.4 18.0 1.0 CZ A:ARG397 4.5 10.3 1.0 NH1 A:ARG443 4.5 19.4 1.0 NE A:ARG397 4.6 10.9 1.0 CG A:TYR320 4.6 17.4 1.0 CZ A:ARG443 4.8 18.2 1.0 O A:ASP396 4.8 15.4 1.0 N A:PRO398 4.9 13.7 1.0 O A:HOH604 4.9 27.9 1.0 CB A:ARG397 4.9 13.0 1.0 O A:TYR320 4.9 17.2 1.0 CG A:ARG397 5.0 13.1 1.0

T.Shinozuka, T.Tsukada, K.Fujii, E.Tokumaru, K.Shimada, Y.Onishi, Y.Matsui, S.Wakimoto, M.Kuroha, T.Ogata, K.Araki, J.Ohsumi, R.Sawamura, N.Watanabe, H.Yamamoto, K.Fujimoto, Y.Tani, M.Mori, J.Tanaka. Discovery of Ds-6930, A Potent Selective Ppar Gamma Modulator. Part I: Lead Identification. Bioorg. Med. Chem. V. 26 5079 2018.
ISSN: ESSN 1464-3391
PubMed: 30241907
DOI: 10.1016/J.BMC.2018.09.006