SMTL ID : 9ijt.1

Crystal Structure of human Programmed cell death 1 ligand 1 (PD-L1) bound to Small molecule inhibitor Compound-10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

2 x 01: (2~{S})-1-[[4-methoxy-2-[(2-methyl-3-phenyl-phenyl)methoxy]pyrimidin-5-yl]methyl]piperidine-2-carboxylic acid

01.1: 18 residues within 4Å: Chain A: I.38, Y.40, Q.50, T.60, M.99, I.100, S.101, A.105, D.106 Chain B: F.3, T.4, Y.40, M.99, I.100, S.101, A.105, D.106, Y.107 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.38, A:Y.40, A:Y.40, A:T.60, A:M.99, A:A.105, B:M.99, B:A.105 Hydrogen bonds: A:Q.50 Water bridges: B:K.108 Salt bridges: B:D.106, B:K.108 pi-Stacking: B:Y.40 01.2: 17 residues within 4Å: Chain C: I.38, Y.40, M.99, I.100, S.101, A.105, D.106 Chain D: A.2, F.3, T.4, Y.40, M.99, I.100, S.101, A.105, D.106, Y.107 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:M.99, D:A.105, D:Y.107, C:I.38, C:Y.40, C:M.99, C:A.105 Hydrogen bonds: D:A.105 Salt bridges: D:D.106 pi-Stacking: D:Y.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Swaminathan, S. et al., Crystal Structure of human Programmed cell death 1 ligand 1 (PD-L1) bound to Small molecule inhibitor Compound-20. To Be Published

Release Date

2025-07-02

Peptides

Programmed cell death 1 ligand 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Programmed cell death 1 ligand 1

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