SMTL ID : 9i0u.1

Structure of human PD-L1 in complex with clinically evaluated inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: R.72, L.73, L.74, K.75, D.76 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.72, A:K.75, A:K.75, A:K.75, A:D.76, A:D.76 Water bridges: A:Q.77 GOL.2: 4 residues within 4Å: Chain B: R.72, L.74, K.75, D.76 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.72, B:R.72, B:K.75

1 x 01: (5~{S})-5-[[[5-[2-chloranyl-3-[2-chloranyl-3-[6-methoxy-5-[[[(2~{S})-5-oxidanylidenepyrrolidin-2-yl]methylamino]methyl]pyrazin-2-yl]phenyl]phenyl]-3-methoxy-pyrazin-2-yl]methylamino]methyl]pyrrolidin-2-one

01.3: 23 residues within 4Å: Chain A: I.40, Y.42, Q.52, M.101, I.102, S.103, A.107, D.108, Y.109, K.110, R.111 Chain B: I.40, Y.42, N.49, Q.52, V.54, M.101, I.102, S.103, A.107, D.108, Y.109, K.110 19 PLIP interactions: 11 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:I.40, A:Y.42, A:M.101, A:A.107, A:K.110, B:I.40, B:M.101, B:A.107 Hydrogen bonds: A:N.49, A:Q.52, A:Y.109, B:N.49, B:Q.52, B:D.108, B:Y.109 Water bridges: A:D.108, A:D.108 pi-Stacking: A:Y.42, B:Y.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Slota, A. et al., Characterization of Clinically Evaluated Small-Molecule Inhibitors of PD-L1 for Immunotherapy. Acs Med.Chem.Lett. (2025)

Release Date

2025-06-18

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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