9LJ3 | pdb_00009lj3

Crystal structure of P25


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 
    0.285 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.243 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery and Crystallography Study of Novel Resorcinol Dibenzyl Ether-Based PD-1/PD-L1 Inhibitors with Improved Drug-like and Pharmacokinetic Properties for Cancer Treatment.

Yang, Z.Yang, P.Xu, J.Yang, X.Zhou, J.He, H.Li, L.Ren, Y.Chen, M.Xiao, Y.Chen, J.

(2025) J Med Chem 68: 12593-12614

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00344
  • Primary Citation of Related Structures:  
    9LJ3

  • PubMed Abstract: 

    Current studies on PD-1/PD-L1 small-molecule inhibitors mainly focus on modifying the linker region between the biphenyl ring and amino acid side chains, or transforming the biphenyl ring into a benzodioxane structure. Herein, we designed and synthesized a series of compounds by introducing a tail at the terminal phenyl ring as small-molecule PD-1/PD-L1 inhibitors. Among them, compound NPH16 exhibited the most potent PD-L1 inhibitory activity (IC 50 = 24.4 nM). The X-ray crystal structure further confirmed the high binding affinity of NPH16 to PD-L1 dimer. In the HepG2/Jurkat T cell coculture model, NPH16 promoted HepG2 cell apoptosis dose-dependently. In addition, NPH16 showed excellent in vivo antitumor efficacy (TGI = 92.1%) in a Hepa1-6 mouse tumor model and increased CD8 + cells in tumor microenvironment. Importantly, NPH16 possessed favorable pharmacokinetic properties with an oral bioavailability of 15.9%. Collectively, compound NPH16 represents a promising PD-1/PD-L1 inhibitor worthy of further investigation as a potential anticancer agent.


  • Organizational Affiliation
    • Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Programmed cell death 1 ligand 1123Homo 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
A1EJ6
Query on A1EJ6

Download Ideal Coordinates CCD File 
G [auth A],
H [auth D],
I [auth E]
3-[[4-chloranyl-2-[(2-hydroxyethylamino)methyl]-5-[[2-methyl-3-[3-[2-[2-[(3~{R})-3-oxidanylpyrrolidin-1-yl]ethoxy]ethoxy]phenyl]phenyl]methoxy]phenoxy]methyl]benzenecarbonitrile
C39 H44 Cl N3 O6
NXKSKHKWKCOEGY-UUWRZZSWSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free:  0.285 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.243 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.422α = 90
b = 77.159β = 97.98
c = 78.099γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Database references
  • Version 1.2: 2025-07-09
    Changes: Database references