SMTL ID : 6r3k.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 2.20 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: A.104, D.105 Chain B: I.37, Y.39, Q.49, V.51 Ligands: JQT.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.105

1 x 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(Non-covalent)

JQT.2: 22 residues within 4Å: Chain A: I.37, Y.39, Q.49, V.51, M.98, S.100, A.104, D.105 Chain B: A.1, F.2, 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 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:M.98, B:A.104, B:Y.106, A:I.37, A:Y.39, A:Y.39, A:M.98, A:A.104 Hydrogen bonds: B:R.108 Water bridges: B:F.2, B:K.107 Salt bridges: B:D.105, B:K.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muszak, D. et al., Terphenyl-Based Small-Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1 Protein-Protein Interaction. J.Med.Chem. (2021)

Release Date

2019-04-03

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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