Structure of human programmed cell death 1 ligand 1 (pd-L1) with low molecular mass inhibitor

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 44% strand (DSSP).

Ligands and binding sites

• JQT · (2~{S},4~{R})-1-[[5-chloranyl-2-[(3-cyanophenyl) methoxy]-4-[[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methyl-phenyl]methoxy]phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxylic acid · ligand · 2 copies · chains A, B, C, D
• EDO · 1,2-ethanediol · additive · 2 copies · chains A, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• B–C · 593 Ų buried · 8 hydrogen bonds · protein-protein
• A–D · 567 Ų buried · 6 hydrogen bonds · protein-protein
• A–B · 435 Ų buried · 6 hydrogen bonds · protein-protein
• C–D · 419 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

• 6R3K · Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q9NZQ7
• Elsewhere: RCSB PDB 6R3K · PDBe 6R3K · UniProt Q9NZQ7