9INU | pdb_00009inu

Novel PD-L1/VISTA dual inhibitor as potential immunotherapy agents


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.287 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

Novel PD-L1/VISTA Dual Inhibitor as Potential Immunotherapy Agents.

Sun, C.Cheng, Y.Dong, J.Hu, L.Zhang, Y.Shen, H.Zhang, G.Jiang, B.Adam Youssouf, S.Min, W.Shen, Y.Wang, L.Deng, H.Xiao, Y.Yang, P.

(2025) J Med Chem 68: 156-173

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01640
  • Primary Citation Related Structures: 
    9INU

  • PubMed Abstract: 

    Inhibiting the activity of immune checkpoint proteins to reignite the antitumor activity of immune cells has emerged as a pivotal strategy. PD-L1 and VISTA, as critical proteins governing immune regulation, are concurrently upregulated under conditions such as hypoxia. Through a rational drug design process, P17 , a dual-target inhibitor for PD-L1 and VISTA is identified. This inhibitor blocks the signaling pathways of both PD-L1 and VISTA at the protein and cellular levels, thereby reactivating the antitumor function of T cells. P17 displays encouraging attributes in terms of druggability and safety assessments. Notably, P17 demonstrates superior antitumor efficacy compared to single-target inhibitors at equivalent doses in in vivo experiments. More crucially, P17 significantly enhances the infiltration of immune cells. This study not only validates the effectiveness of a dual-target inhibitor strategy against PD-L1 and VISTA, but also identifies P17 as a promising candidate molecule with significant therapeutic potential.


  • Organizational Affiliation
    • State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.

Macromolecule Content 

  • Total Structure Weight: 29.77 kDa 
  • Atom Count: 1,980 
  • Modeled Residue Count: 251 
  • Deposited Residue Count: 256 
  • 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
128Homo 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
A1D9R

Query on A1D9R



Download:Ideal Coordinates CCD File
C [auth B](2~{S})-2-[[6-methoxy-2-[(2-methyl-3-phenyl-phenyl)amino]pyrimidin-4-yl]methylamino]-3-oxidanyl-propanoic acid
C22 H24 N4 O4
QSHNMTVUJAVARU-IBGZPJMESA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.287 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.096α = 90
b = 83.603β = 90
c = 96.838γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release