8OR1 | pdb_00008or1

Co-crystal strucutre of PD-L1 with low molecular weight inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.296 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.292 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 
    0.293 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design, Synthesis, and Antitumor Activity Evaluation of 2-Arylmethoxy-4-(2,2'-dihalogen-substituted biphenyl-3-ylmethoxy) Benzylamine Derivatives as Potent PD-1/PD-L1 Inhibitors.

Zhang, H.Zhou, S.Plewka, J.Wu, C.Zhu, M.Yu, Q.Musielak, B.Wang, X.Awadasseid, A.Magiera-Mularz, K.Wu, Y.Zhang, W.

(2023) J Med Chem 66: 10579-10603

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00731
  • Primary Citation of Related Structures:  
    8OR1

  • PubMed Abstract: 

    Novel 2-arylmethoxy-4-(2,2'-dihalogen-substituted biphenyl-3-ylmethoxy) benzylamine derivatives were designed, synthesized, and evaluated in vitro and in vivo against cancers as PD-1/PD-L1 inhibitors. Through the computer-aided structural optimization and the homogeneous time-resolved fluorescence (HTRF) assay, compound A56 was found to most strongly block the PD-1/PD-L1 interaction with an IC 50 value of 2.4 ± 0.8 nM and showed the most potent activity. 1 H NMR titration results indicated that A56 can tightly bind to the PD-L1 protein with K D < 1 μM. The X-ray diffraction data for the cocrystal structure of the A56/ PD-L1 complex (3.5 Å) deciphered a novel binding mode in detail, which can account for its most potent inhibitory activity. Cell-based assays further demonstrated the strong ability of A56 as an hPD-1/hPD-L1 blocker. Especially in an hPD-L1 MC38 humanized mouse model, A56 significantly inhibited tumor growth without obvious toxicity, with a TGI rate of 55.20% (50 mg/kg, i.g.). In conclusion, A56 is a promising clinical candidate worthy of further development.


  • Organizational Affiliation
    • Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Programmed cell death 1 ligand 1
A, B
116Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VYC (Subject of Investigation/LOI)
Query on VYC

Download Ideal Coordinates CCD File 
C [auth A]5-[[5-[[2-chloranyl-3-(2-fluorophenyl)phenyl]methoxy]-2-[(~{E})-2-hydroxyethyliminomethyl]phenoxy]methyl]pyridine-3-carbonitrile
C29 H25 Cl F N3 O3
DSELNKYPNSPLEU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.296 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.292 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 0.293 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.459α = 90
b = 73.459β = 90
c = 95.156γ = 120
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
National Natural Science Foundation of China (NSFC)China21877101
Foundation for Polish SciencePolandTEAM TECH CORE FACILITY/2017-4/6
National Natural Science Foundation of China (NSFC)China22177105

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-02
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-13
    Changes: Structure summary