SMTL ID : 8r6q.1

Co-crystal structure of PD-L1 with low molecular weight inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-dimer

Ligands

1 x WEW: (3~{R})-1-[[4-[2-chloranyl-3-(2,3-dihydro-1,4-benzodioxin-6-yl)phenyl]-2-methoxy-phenyl]methyl]-~{N}-(2-hydroxyethyl)pyrrolidine-3-carboxamide(Non-covalent)

WEW.1: 17 residues within 4Å: Chain A: I.37, Y.39, Q.49, M.98, I.99, S.100, A.104, D.105, Y.106 Chain B: I.37, Y.39, M.98, A.104, D.105, Y.106, K.107, R.108 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:M.98, B:Y.106, A:I.37, A:Y.39, A:M.98, A:A.104 Hydrogen bonds: B:R.108 Water bridges: B:Y.106 Salt bridges: B:D.105 pi-Stacking: A:Y.39

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: P.7, K.8, Y.11, E.22 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain B: P.7, K.8, Y.11, E.22 Ligand excluded by PLIP

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: R.69, L.71, K.72, D.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.72, A:D.73 Salt bridges: A:R.69 SO4.5: 5 residues within 4Å: Chain B: R.69, L.70, L.71, K.72, D.73 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.72, B:D.73, B:D.73 Salt bridges: B:R.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Surmiak, E. et al., Solubilizer Tag Effect on PD-L1/Inhibitor Binding Properties for m -Terphenyl Derivatives. Acs Med.Chem.Lett. (2024)

Release Date

2024-01-17

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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