SMTL ID : 6vqn.2 (1 other biounit)

Co-crystal structure of human PD-L1 complexed with Compound A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-dimer

Ligands

2 x R81: N,N'-(2,2'-dimethyl[1,1'-biphenyl]-3,3'-diyl)bis(5-{[(2-hydroxyethyl)amino]methyl}pyridine-2-carboxamide)(Non-covalent)

R81.1: 12 residues within 4Å: Chain A: T.4, V.5, A.105, D.106, Y.107 Chain B: I.38, Y.40, Q.50, M.99, I.100, S.101 Ligands: R81.2 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.38, B:Y.40, B:M.99, A:A.105, A:Y.107 pi-Stacking: B:Y.40 Hydrogen bonds: A:V.5, A:D.106, A:K.108 Water bridges: A:A.105 R81.2: 12 residues within 4Å: Chain A: I.38, Y.40, Q.50, M.99, I.100, S.101 Chain B: T.4, V.5, A.105, D.106, Y.107 Ligands: R81.1 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.105, B:Y.107, A:I.38, A:Y.40, A:M.99 Hydrogen bonds: B:V.5, B:K.108 Water bridges: B:A.105 pi-Stacking: A:Y.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J.J. et al., Checkpoint inhibition through small molecule-induced internalization of programmed death-ligand 1. Nat Commun (2021)

Release Date

2021-01-20

Peptides

Programmed cell death 1 ligand 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

Programmed cell death 1 ligand 1

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