SMTL ID : 5niu.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: A.104, D.105 Chain B: Y.39, Q.49 Ligands: 8YZ.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.104, A:D.105 Water bridges: A:Y.106

1 x 8YZ: (2~{R})-2-[[2-[(3-cyanophenyl)methoxy]-4-[[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methyl-phenyl]methoxy]-5-methyl-phenyl]methylamino]-3-oxidanyl-propanoic acid(Non-covalent)

8YZ.2: 22 residues within 4Å: Chain A: I.37, Y.39, D.44, Q.49, V.51, M.98, I.99, S.100, A.104, D.105 Chain B: T.3, I.37, Y.39, M.98, I.99, S.100, A.104, D.105, Y.106, K.107, R.108 Ligands: EDO.1 14 PLIP interactions: 6 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:Y.39, A:Y.39, A:Q.49, A:V.51, A:M.98, B:M.98, B:A.104, B:Y.106, B:K.107 Hydrogen bonds: A:Y.39, B:D.105, B:K.107 Water bridges: B:Y.106 pi-Stacking: B:Y.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skalniak, L. et al., Small-molecule inhibitors of PD-1/PD-L1 immune checkpoint alleviate the PD-L1-induced exhaustion of T-cells. Oncotarget (2017)

Release Date

2017-12-06

Peptides

Programmed cell death 1 ligand 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Programmed cell death 1 ligand 1

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