Chlorine in PDB 7nld: Structure of Human Programmed Cell Death 1 Ligand 1 (Pd-L1) with Low Molecular Mass Inhibitor

The structure of Structure of Human Programmed Cell Death 1 Ligand 1 (Pd-L1) with Low Molecular Mass Inhibitor, PDB code: 7nld was solved by D.Sala, K.Magiera-Mularz, D.Muszak, E.Surmiak, P.Grudnik, T.A.Holak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.03 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.087, 75.255, 74.354, 90, 96.29, 90
R / Rfree (%)	24.3 / 29.4

The binding sites of Chlorine atom in the Structure of Human Programmed Cell Death 1 Ligand 1 (Pd-L1) with Low Molecular Mass Inhibitor (pdb code 7nld). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Structure of Human Programmed Cell Death 1 Ligand 1 (Pd-L1) with Low Molecular Mass Inhibitor, PDB code: 7nld:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Structure of Human Programmed Cell Death 1 Ligand 1 (Pd-L1) with Low Molecular Mass Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Human Programmed Cell Death 1 Ligand 1 (Pd-L1) with Low Molecular Mass Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:63.3 occ:1.00 CL A:UGZ201 0.0 63.3 1.0 C A:UGZ201 1.7 56.3 1.0 C16 A:UGZ201 2.7 51.6 1.0 C1 A:UGZ201 2.7 51.1 1.0 O A:ASP122 3.1 51.7 1.0 C2 A:UGZ201 3.1 56.8 1.0 C17 A:UGZ201 3.1 51.0 1.0 C12 A:UGZ201 3.1 58.9 1.0 C18 A:UGZ201 3.2 48.9 1.0 C A:ASP122 3.3 55.0 1.0 N A:ASP122 3.6 55.0 1.0 CA A:ASP122 3.8 52.4 1.0 C13 A:UGZ201 4.0 53.9 1.0 C15 A:UGZ201 4.0 51.8 1.0 CB A:TYR123 4.0 49.0 1.0 N A:TYR123 4.0 50.1 1.0 CB A:ALA121 4.1 49.4 1.0 C20 A:UGZ201 4.2 46.5 1.0 C3 A:UGZ201 4.2 62.6 1.0 CB A:MET115 4.2 45.9 1.0 C11 A:UGZ201 4.3 66.4 1.0 C A:ALA121 4.3 56.5 1.0 C19 A:UGZ201 4.3 51.8 1.0 O A:ILE116 4.4 56.5 1.0 SD B:MET115 4.4 49.4 1.0 CD1 A:TYR123 4.5 47.7 1.0 C14 A:UGZ201 4.5 54.9 1.0 CA A:TYR123 4.6 50.1 1.0 N A:ILE116 4.6 48.6 1.0 CA A:MET115 4.6 38.2 1.0 CA A:ALA121 4.7 53.6 1.0 CG A:MET115 4.7 39.8 1.0 CG A:TYR123 4.7 47.4 1.0 C A:MET115 4.9 46.4 1.0

Chlorine binding site 2 out of 3 in the Structure of Human Programmed Cell Death 1 Ligand 1 (Pd-L1) with Low Molecular Mass Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Human Programmed Cell Death 1 Ligand 1 (Pd-L1) with Low Molecular Mass Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl201 b:68.5 occ:1.00 CL D:UGZ201 0.0 68.5 1.0 C D:UGZ201 1.7 62.9 1.0 C16 D:UGZ201 2.7 61.1 1.0 C1 D:UGZ201 2.7 57.6 1.0 C12 D:UGZ201 3.1 55.9 1.0 C17 D:UGZ201 3.1 65.2 1.0 C2 D:UGZ201 3.1 53.0 1.0 O C:ASP122 3.1 56.8 1.0 C18 D:UGZ201 3.1 68.8 1.0 C C:ASP122 3.4 60.4 1.0 N C:ASP122 3.4 56.8 1.0 CA C:ASP122 3.8 55.5 1.0 CB C:ALA121 3.9 54.3 1.0 C15 D:UGZ201 4.0 61.0 1.0 C13 D:UGZ201 4.0 57.0 1.0 CB C:MET115 4.0 51.0 1.0 N C:TYR123 4.1 55.5 1.0 C C:ALA121 4.1 58.5 1.0 C20 D:UGZ201 4.1 69.0 1.0 CB C:TYR123 4.1 45.3 1.0 C19 D:UGZ201 4.2 69.9 1.0 C11 D:UGZ201 4.3 64.0 1.0 C3 D:UGZ201 4.3 63.4 1.0 O C:ILE116 4.3 61.8 1.0 SD D:MET115 4.4 51.7 1.0 N C:ILE116 4.4 53.1 1.0 CA C:ALA121 4.5 54.4 1.0 C14 D:UGZ201 4.5 59.0 1.0 CA C:MET115 4.5 46.6 1.0 CA C:TYR123 4.6 49.2 1.0 CG C:MET115 4.6 43.9 1.0 C C:MET115 4.8 54.4 1.0 CD1 C:TYR123 4.8 49.6 1.0 O C:ALA121 4.9 64.2 1.0 CG C:TYR123 4.9 50.8 1.0 C21 D:UGZ201 5.0 95.9 1.0 CB D:MET115 5.0 48.5 1.0

Chlorine binding site 3 out of 3 in the Structure of Human Programmed Cell Death 1 Ligand 1 (Pd-L1) with Low Molecular Mass Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Human Programmed Cell Death 1 Ligand 1 (Pd-L1) with Low Molecular Mass Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl201 b:74.2 occ:1.00 CL E:UGZ201 0.0 74.2 1.0 C E:UGZ201 1.7 62.4 1.0 C16 E:UGZ201 2.7 59.2 1.0 C1 E:UGZ201 2.7 57.6 1.0 C12 E:UGZ201 3.1 61.0 1.0 C17 E:UGZ201 3.1 55.5 1.0 C2 E:UGZ201 3.1 60.3 1.0 C20 E:UGZ201 3.3 58.6 1.0 C15 E:UGZ201 4.0 52.1 1.0 C13 E:UGZ201 4.0 55.6 1.0 C18 E:UGZ201 4.1 54.2 1.0 SD E:MET115 4.3 62.5 1.0 C11 E:UGZ201 4.3 68.2 1.0 C3 E:UGZ201 4.3 60.7 1.0 C14 E:UGZ201 4.5 57.1 1.0 C21 E:UGZ201 4.5 59.4 1.0 CB E:MET115 5.0 53.6 1.0

D.Muszak, E.Surmiak, J.Plewka, K.Magiera-Mularz, J.Kocik-Krol, B.Musielak, D.Sala, R.Kitel, M.Stec, K.Weglarczyk, M.Siedlar, A.Domling, L.Skalniak, T.A.Holak. Terphenyl-Based Small-Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1 Protein-Protein Interaction. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34313116
DOI: 10.1021/ACS.JMEDCHEM.1C00957