SMTL ID : 5niu.1 (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 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.1: 22 residues within 4Å: Chain A: T.3, I.37, Y.39, M.98, I.99, S.100, A.104, D.105, Y.106, K.107, R.108 Chain B: I.37, Y.39, Q.49, V.51, M.98, I.99, S.100, A.104, D.105, Y.106 Ligands: EDO.2 16 PLIP interactions: 9 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:Y.39, B:Y.39, B:Q.49, B:V.51, B:M.98, A:M.98, A:A.104, A:Y.106, A:Y.106 Hydrogen bonds: B:Q.49, A:D.105, A:K.107, A:K.107 Water bridges: B:N.46, B:N.46, B:N.46

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

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

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
A

B
B

Programmed cell death 1 ligand 1

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