Structure of human Programmed cell death 1 ligand 1 (PD-L1) with inhibitor

Experimental Data Snapshot

  • Resolution: 2.45 Å
  • R-Value Work: 0.274 

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Design, Synthesis, and Biological Evaluation of Imidazopyridines as PD-1/PD-L1 Antagonists.

Butera, R.Wazynska, M.Magiera-Mularz, K.Plewka, J.Musielak, B.Surmiak, E.Sala, D.Kitel, R.de Bruyn, M.Nijman, H.W.Elsinga, P.H.Holak, T.A.Domling, A.

(2021) ACS Med Chem Lett 12: 768-773

  • DOI: https://doi.org/10.1021/acsmedchemlett.1c00033
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The PD-1/PD-L1 axis has proven to be a highly efficacious target for cancer immune checkpoint therapy with several approved antibodies. Also, small molecules based on a biphenyl core can antagonize PD-1/PD-L1, leading to the in vitro formation of PD-L1 dimers. However, their development remains challenging, as we do not yet fully understand their mode of action. In this work, we designed a new scaffold based on our previously solved high-resolution structures of low-molecular-weight inhibitors bound to PD-L1. A small compound library was synthesized using the Groebke-Blackburn-Bienaymé multicomponent reaction (GBB-3CR), resulting in the structure-activity relationship of imidazo[1,2- a ]pyridine-based inhibitors. These inhibitors were tested for their biological activity using various biophysical assays giving potent candidates with low-micromolar PD-L1 affinities. An obtained PD-L1 cocrystal structure reveals the binding to PD-L1. Our results open the door to an interesting bioactive scaffold that could lead to a new class of PD-L1 antagonists.

  • Organizational Affiliation

    Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  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
GTEx:  ENSG00000120217 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZQ7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TK2 (Subject of Investigation/LOI)
Query on TK2

Download Ideal Coordinates CCD File 
C [auth A]2-(aminomethyl)-6-[(2-methyl-3-phenyl-phenyl)methoxy]-~{N}-(2-phenylethyl)imidazo[1,2-a]pyridin-3-amine
C30 H30 N4 O
Experimental Data & Validation

Experimental Data

  • Resolution: 2.45 Å
  • R-Value Work: 0.274 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.617α = 90
b = 54.616β = 90
c = 140.962γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description