9HRT | pdb_00009hrt

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.263 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 30.44 kDa 
  • Atom Count: 2,100 
  • Modeled Residue Count: 252 
  • Deposited Residue Count: 262 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IXH
(Subject of Investigation/LOI)

Query on A1IXH



Download:Ideal Coordinates CCD File
C [auth B](2~{R})-2-[[3-[(~{E})-2-[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methyl-phenyl]ethenyl]-4-(trifluoromethyl)phenyl]methylamino]-2-methyl-3-oxidanyl-propanoic acid
C29 H28 F3 N O5
PTGUEPRQUFAZLN-UWSNOUECSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.263 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.859α = 90
b = 52.03β = 90
c = 111.318γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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