Chlorine in PDB 6nos: Pd-L1 Igv Domain V76T with Fragment

The structure of Pd-L1 Igv Domain V76T with Fragment, PDB code: 6nos was solved by B.Zhao, E.Perry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.42 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	84.014, 97.401, 33.182, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 27.5

The binding sites of Chlorine atom in the Pd-L1 Igv Domain V76T with Fragment (pdb code 6nos). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Pd-L1 Igv Domain V76T with Fragment, PDB code: 6nos:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Pd-L1 Igv Domain V76T with Fragment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Pd-L1 Igv Domain V76T with Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl400 b:49.3 occ:1.00 CL2 A:KWA400 0.0 49.3 1.0 C10 A:KWA400 1.8 43.2 1.0 C11 A:KWA400 2.6 28.2 1.0 C07 A:KWA400 2.8 44.6 1.0 N A:SER117 3.3 21.7 1.0 O A:MET115 3.3 18.4 1.0 O A:ILE54 3.3 33.5 1.0 C A:MET115 3.5 17.6 1.0 C A:ILE116 3.5 35.6 1.0 N A:ILE116 3.6 22.4 1.0 CA A:ILE116 3.6 31.5 1.0 CB A:SER117 3.8 33.0 1.0 CG2 A:ILE54 3.8 24.6 1.0 C A:ILE54 3.8 28.3 1.0 CB A:ILE54 3.8 24.3 1.0 C09 A:KWA400 3.9 31.6 1.0 N A:TYR56 3.9 21.5 1.0 CD1 A:TYR56 4.1 44.7 1.0 C03 A:KWA400 4.1 44.1 1.0 CB A:MET115 4.1 16.0 1.0 CA A:SER117 4.1 22.9 1.0 O A:ILE116 4.2 47.7 1.0 N A:VAL55 4.4 21.5 1.0 CA A:MET115 4.4 16.3 1.0 CA A:ILE54 4.4 23.2 1.0 CB A:TYR56 4.5 32.6 1.0 CA A:VAL55 4.5 23.7 1.0 C08 A:KWA400 4.5 36.6 1.0 CG A:TYR56 4.6 41.6 1.0 C A:VAL55 4.6 21.1 1.0 CA A:TYR56 4.8 22.0 1.0 CE1 A:TYR56 4.8 36.0 1.0

Chlorine binding site 2 out of 2 in the Pd-L1 Igv Domain V76T with Fragment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Pd-L1 Igv Domain V76T with Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl400 b:61.1 occ:1.00 CL3 A:KWA400 0.0 61.1 1.0 C09 A:KWA400 1.8 31.6 1.0 C11 A:KWA400 2.6 28.2 1.0 C08 A:KWA400 2.9 36.6 1.0 CA B:ASP122 3.2 44.6 1.0 CZ A:TYR56 3.3 45.7 1.0 C B:ASP122 3.3 29.6 1.0 CE2 A:TYR56 3.4 42.0 1.0 CD2 B:TYR123 3.6 38.0 1.0 N B:TYR123 3.6 25.2 1.0 OH A:TYR56 3.6 42.2 1.0 CE1 A:TYR56 3.7 36.0 1.0 O B:ASP122 3.7 29.2 1.0 N B:ASP122 3.7 39.9 1.0 O B:ALA121 3.8 32.8 1.0 C10 A:KWA400 3.9 43.2 1.0 C B:ALA121 3.9 38.5 1.0 CD2 A:TYR56 3.9 37.7 1.0 OD1 B:ASP122 4.0 60.2 1.0 CD1 A:TYR56 4.1 44.7 1.0 C03 A:KWA400 4.1 44.1 1.0 CB B:TYR123 4.3 27.3 1.0 CG A:TYR56 4.3 41.6 1.0 CG B:TYR123 4.4 32.6 1.0 CE2 B:TYR123 4.5 53.1 1.0 CB B:ASP122 4.5 45.5 1.0 C07 A:KWA400 4.5 44.6 1.0 CA B:TYR123 4.5 28.7 1.0 CB B:ALA121 4.6 55.5 1.0 CE A:MET115 4.6 39.6 1.0 CG B:ASP122 4.7 56.3 1.0 CA B:ALA121 4.9 44.7 1.0

E.Perry, J.J.Mills, B.Zhao, F.Wang, Q.Sun, P.P.Christov, J.C.Tarr, T.A.Rietz, E.T.Olejniczak, T.Lee, S.Fesik. Fragment-Based Screening of Programmed Death Ligand 1 (Pd-L1). Bioorg. Med. Chem. Lett. V. 29 786 2019.
ISSN: ESSN 1464-3405
PubMed: 30728114
DOI: 10.1016/J.BMCL.2019.01.028