8P1O | pdb_00008p1o

Solubilizer tag effect on PD-L1/inhibitor binding properties for m-terphenyl derivatives


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 
    0.289 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.271 (Depositor), 0.271 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Solubilizer Tag Effect on PD-L1/Inhibitor Binding Properties for m -Terphenyl Derivatives.

Surmiak, E.Zaber, J.Plewka, J.Wojtanowicz, G.Kocik-Krol, J.Kruc, O.Muszak, D.Rodriguez, I.Musielak, B.Viviano, M.Castellano, S.Skalniak, L.Magiera-Mularz, K.Holak, T.A.Kalinowska-Tluscik, J.

(2024) ACS Med Chem Lett 15: 36-44

  • DOI: https://doi.org/10.1021/acsmedchemlett.3c00306
  • Primary Citation Related Structures: 
    8P1O

  • PubMed Abstract: 

    Although heavily studied, the subject of anti-PD-L1 small-molecule inhibitors is still elusive. Here we present a systematic overview of the principles behind successful anti-PD-L1 small-molecule inhibitor design on the example of the m -terphenyl scaffold, with a particular focus on the neglected influence of the solubilizer tag on the overall affinity toward PD-L1. The inhibitor developed according to the proposed guidelines was characterized through its potency in blocking PD-1/PD-L1 complex formation in homogeneous time-resolved fluorescence and cell-based assays. The affinity is also explained based on the crystal structure of the inhibitor itself and its costructure with PD-L1 as well as a molecular modeling study. Our results structuralize the knowledge related to the strong pharmacophore feature of the m -terphenyl scaffold preferential geometry and the more complex role of the solubilizer tag in PD-L1 homodimer stabilization.


  • Organizational Affiliation
    • Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland.

Macromolecule Content 

  • Total Structure Weight: 34.25 kDa 
  • Atom Count: 2,119 
  • Modeled Residue Count: 252 
  • Deposited Residue Count: 288 
  • 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
144Homo 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: 2.17 Å
  • R-Value Free:  0.289 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.271 (Depositor), 0.271 (DCC) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.088α = 90
b = 109.991β = 90
c = 51.823γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePolandUMO-2020/39/D/ST4/01344

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Structure summary
  • Version 1.2: 2025-12-03
    Changes: Advisory