Chlorine in PDB 8r6q: Co-Crystal Structure of Pd-L1 with Low Molecular Weight Inhibitor

The structure of Co-Crystal Structure of Pd-L1 with Low Molecular Weight Inhibitor, PDB code: 8r6q was solved by J.Plewka, E.Surmiak, K.Magiera-Mularz, J.Kalinowska-Tluscik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.88 / 2.17
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	52.088, 109.991, 51.823, 90, 90, 90
R / Rfree (%)	27.1 / 28.9

The binding sites of Chlorine atom in the Co-Crystal Structure of Pd-L1 with Low Molecular Weight Inhibitor (pdb code 8r6q). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Co-Crystal Structure of Pd-L1 with Low Molecular Weight Inhibitor, PDB code: 8r6q:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Co-Crystal Structure of Pd-L1 with Low Molecular Weight Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Co-Crystal Structure of Pd-L1 with Low Molecular Weight Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:51.2 occ:1.00 CL1 A:WEW201 0.0 51.2 1.0 C17 A:WEW201 1.7 33.6 1.0 C18 A:WEW201 2.7 41.2 1.0 C16 A:WEW201 2.7 42.9 1.0 C22 A:WEW201 3.1 50.2 1.0 C13 A:WEW201 3.1 47.6 1.0 C14 A:WEW201 3.1 47.3 1.0 O B:ASP121 3.3 22.1 1.0 C29 A:WEW201 3.3 44.9 1.0 C B:ASP121 3.5 21.8 1.0 N B:ASP121 3.7 22.2 1.0 CA B:ASP121 3.8 22.3 1.0 C19 A:WEW201 4.0 37.7 1.0 C21 A:WEW201 4.0 43.5 1.0 C23 A:WEW201 4.0 42.0 1.0 N B:TYR122 4.0 20.5 1.0 CB B:TYR122 4.2 25.4 1.0 CG B:MET114 4.2 36.2 1.0 C12 A:WEW201 4.3 61.4 1.0 CB B:MET114 4.3 32.1 1.0 CB B:ALA120 4.3 23.6 1.0 C15 A:WEW201 4.3 50.2 1.0 C28 A:WEW201 4.3 46.7 1.0 C B:ALA120 4.3 23.0 1.0 SD A:MET114 4.4 37.3 1.0 CD1 B:TYR122 4.5 31.2 1.0 CE B:MET114 4.5 34.6 1.0 C20 A:WEW201 4.5 45.9 1.0 O B:ILE115 4.7 23.6 1.0 CA B:MET114 4.7 31.3 1.0 CA B:TYR122 4.7 28.5 1.0 CG B:TYR122 4.8 28.2 1.0 CA B:ALA120 4.8 24.5 1.0 N B:ILE115 4.8 28.8 1.0 CB A:MET114 4.9 32.9 1.0 C24 A:WEW201 4.9 48.6 1.0 O B:ALA120 4.9 19.3 1.0 CG A:MET114 5.0 34.5 1.0

Chlorine binding site 2 out of 3 in the Co-Crystal Structure of Pd-L1 with Low Molecular Weight Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Co-Crystal Structure of Pd-L1 with Low Molecular Weight Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:74.7 occ:1.00 OH A:TYR27 2.6 19.5 1.0 O A:LYS24 2.8 30.3 1.0 O A:GLU38 2.9 34.0 1.0 N A:LYS24 3.1 29.7 1.0 CD A:PRO23 3.4 29.2 1.0 CZ A:TYR27 3.5 23.7 1.0 CE1 A:TYR27 3.5 22.5 1.0 C A:LYS24 3.6 26.3 1.0 CA A:LYS24 3.6 28.3 1.0 N A:PRO23 3.7 31.2 1.0 N A:GLU38 3.8 34.0 1.0 CB A:LYS24 3.8 30.5 1.0 C A:GLU38 3.8 37.1 1.0 CB A:GLU38 4.0 33.2 1.0 CG A:PRO23 4.1 27.7 1.0 CB A:VAL22 4.1 34.4 1.0 CA A:GLU38 4.1 36.9 1.0 C A:PRO23 4.1 26.5 1.0 C A:VAL22 4.2 31.8 1.0 CB A:PRO23 4.2 25.5 1.0 CD1 A:ILE125 4.3 38.9 1.0 CA A:PRO23 4.3 28.0 1.0 CA A:VAL22 4.3 34.4 1.0 CG1 A:VAL22 4.5 31.8 1.0 CG A:LYS24 4.7 30.7 1.0 CE2 A:TYR27 4.8 25.0 1.0 CD1 A:TYR27 4.8 21.6 1.0 N A:ASP25 4.9 26.2 1.0 CG1 A:ILE125 4.9 34.6 1.0 C A:ILE37 4.9 31.8 1.0 CG2 A:ILE37 4.9 48.9 1.0

Chlorine binding site 3 out of 3 in the Co-Crystal Structure of Pd-L1 with Low Molecular Weight Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Co-Crystal Structure of Pd-L1 with Low Molecular Weight Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:74.7 occ:1.00 OH B:TYR27 2.6 29.4 1.0 O B:GLU38 2.7 32.6 1.0 O B:LYS24 2.8 24.6 1.0 N B:LYS24 3.2 29.5 1.0 CD B:PRO23 3.4 32.1 1.0 CZ B:TYR27 3.5 32.3 1.0 CE1 B:TYR27 3.5 27.8 1.0 CG B:PRO23 3.5 37.0 1.0 C B:GLU38 3.6 31.4 1.0 N B:GLU38 3.6 30.0 1.0 C B:LYS24 3.7 26.3 1.0 CA B:LYS24 3.8 30.5 1.0 N B:PRO23 3.8 30.5 1.0 CA B:GLU38 3.9 31.6 1.0 CB B:LYS24 3.9 33.3 1.0 CB B:GLU38 3.9 29.4 1.0 CB B:VAL22 4.1 27.5 1.0 C B:VAL22 4.3 24.9 1.0 C B:PRO23 4.3 31.6 1.0 CA B:VAL22 4.3 28.6 1.0 CA B:PRO23 4.4 34.4 1.0 CB B:PRO23 4.4 32.9 1.0 CG1 B:VAL22 4.5 26.5 1.0 CG1 B:ILE125 4.8 32.2 1.0 C B:ILE37 4.8 26.3 1.0 CE2 B:TYR27 4.8 29.6 1.0 N B:CYS39 4.8 42.7 1.0 CG2 B:ILE37 4.8 44.4 1.0 CD1 B:TYR27 4.8 29.2 1.0 N B:ASP25 4.9 26.0 1.0 CG B:LYS24 4.9 34.4 1.0

E.Surmiak, J.Zaber, J.Plewka, G.Wojtanowicz, J.Kocik-Krol, O.Kruc, D.Muszak, I.Rodriguez, B.Musielak, M.Viviano, S.Castellano, L.Skalniak, K.Magiera-Mularz, T.A.Holak, J.Kalinowska-Tluscik. Solubilizer Tag Effect on Pd-L1/Inhibitor Binding Properties For M-Terphenyl Derivatives Acs Med.Chem.Lett. 2023.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.3C00306