9I0U | pdb_00009i0u

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 
    0.202 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.172 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Characterization of Clinically Evaluated Small-Molecule Inhibitors of PD-L1 for Immunotherapy.

Slota, A.Golebiowska-Mendroch, K.Kocik-Krol, J.Musielak, B.Stec, M.Weglarczyk, K.Siedlar, M.Skalniak, L.Plewka, J.Magiera-Mularz, K.

(2025) ACS Med Chem Lett 16: 1359-1364

  • DOI: https://doi.org/10.1021/acsmedchemlett.5c00245
  • Primary Citation of Related Structures:  
    9HRT, 9I0U, 9I0W

  • PubMed Abstract: 

    Cancer immunotherapy aims to employ the immune system to target cancer cells. The PD-1/PD-L1 axis is a critical immune checkpoint that tumors exploit to evade immune surveillance. In this study, we characterized three small-molecule PD-L1 inhibitors, Evixapodlin, MAX-10181, and INCB086550, currently undergoing clinical trials for cancers such as non-small cell lung cancer, renal cell carcinoma, urothelial carcinoma, hepatocellular carcinoma, and melanoma. Using the homogeneous time resolved fluorescence assay, we confirmed that each compound potently disrupts human PD-1/PD-L1 binding with IC 50 values in the nanomolar range. PD-L1 oligomerization upon inhibitor binding was demonstrated through NMR analysis and confirmed by X-ray crystallography, which finally elucidated the binding interactions that stabilize these inhibitors at the PD-L1 interface. Cellular assays revealed dose-dependent T-cell activation, demonstrating the immunomodulatory potential of each compound and its cytotoxicity profiles. These findings underscore the promise of small-molecule PD-L1 inhibitors as viable alternatives to antibody-based therapies in cancer immunotherapy.


  • Organizational Affiliation
    • Jagiellonian University, Faculty of Chemistry, Department of Organic Chemistry, Gronostajowa 2, 30-387 Krakow, Poland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Programmed cell death 1 ligand 1
A, B
131Homo sapiensMutation(s): 0 
Gene Names: CD274B7H1PDCD1L1PDCD1LG1PDL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZQ7 (Homo sapiens)
Explore Q9NZQ7 
Go to UniProtKB:  Q9NZQ7
PHAROS:  Q9NZQ7
GTEx:  ENSG00000120217 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZQ7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IZJ (Subject of Investigation/LOI)
Query on A1IZJ

Download Ideal Coordinates CCD File 
E [auth B](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
C34 H36 Cl2 N8 O4
OIIOPWHTJZYKIL-PMACEKPBSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free:  0.202 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.172 (DCC) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.997α = 90
b = 52.405β = 90
c = 112.022γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2021/43/B/NZ7/03170

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release
  • Version 1.1: 2025-07-30
    Changes: Database references