9EO0 | pdb_00009eo0

Small-Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.302 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.253 (Depositor), 0.250 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Nonsymmetrically Substituted 1,1'-Biphenyl-Based Small Molecule Inhibitors of the PD-1/PD-L1 Interaction.

Hec-Galazka, A.Tyrcha, U.Barczynski, J.Bielski, P.Mikitiuk, M.Gudz, G.P.Kitel, R.Musielak, B.Plewka, J.Sitar, T.Holak, T.A.

(2024) ACS Med Chem Lett 15: 828-836

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00042
  • Primary Citation of Related Structures:  
    9EO0

  • PubMed Abstract: 

    Therapeutic antibodies directed against either programmed cell death-1 protein (PD-1) or its ligand PD-L1 have demonstrated efficacy in the treatment of various cancers. In contrast with antibodies, small molecules have the potential for increased tissue penetration; better pharmacology; and therefore, improved antitumor activity. A series of nonsymmetric C2 inhibitors were synthesized and evaluated for PD-1/PD-L1 interaction inhibition. These compounds induced PD-L1 dimerization and effectively blocked PD-L1/PD-1 interaction in a homogeneous time-resolved fluorescence (HTRF) assay with most inhibitors exhibiting IC 50 values in the single-digit nM range and below. Their high inhibitory potency was also demonstrated in a cell-based coculture PD-1 signaling assay where 2 exhibited an EC 50 inhibitory activity of 21.8 nM, which approached that of the PD-L1 antibody durvalumab (EC 50 = 0.3-1.8 nM). Structural insight into how these inhibitors interact with PD-L1 was gained by using NMR and X-ray cocrystal structure studies. These data support further preclinical evaluation of these compounds as antibody alternatives.


  • Organizational Affiliation
    • Jagiellonian University, Doctoral School of Exact and Natural Sciences, prof. S. Łojasiewicza 11, 30-348 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, C, D, E
A, B, C, D, E, F
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.302 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.253 (Depositor), 0.250 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.753α = 90
b = 75.405β = 97.249
c = 75.923γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
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
National Center for Research and Development (Poland)PolandPOIR.01.01.01-00-0129/18

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Structure summary