Structure of PD-L1/small-molecule inhibitor complex

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

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Small-Molecule Inhibitors of the Programmed Cell Death-1/Programmed Death-Ligand 1 (PD-1/PD-L1) Interaction via Transiently Induced Protein States and Dimerization of PD-L1.

Guzik, K.Zak, K.M.Grudnik, P.Magiera, K.Musielak, B.Torner, R.Skalniak, L.Domling, A.Dubin, G.Holak, T.A.

(2017) J Med Chem 60: 5857-5867

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00293
  • Primary Citation of Related Structures:  
    5N2D, 5N2F

  • PubMed Abstract: 

    Blockade of the PD-1/PD-L1 immune checkpoint pathway with monoclonal antibodies has provided significant advances in cancer treatment. The antibody-based immunotherapies carry a number of disadvantages such as the high cost of the antibodies, their limited half-life, and immunogenicity. Development of small-molecule PD-1/PD-L1 inhibitors that could overcome these drawbacks is slow because of the incomplete structural information for this pathway. The first chemical PD-1/PD-L1 inhibitors have been recently disclosed by Bristol-Myers Squibb. Here we present NMR and X-ray characterization for the two classes of these inhibitors. The X-ray structures of the PD-L1/inhibitor complexes reveal one inhibitor molecule located at the center of the PD-L1 homodimer, filling a deep hydrophobic channel-like pocket between two PD-L1 molecules. Derivatives of (2-methyl-3-biphenylyl)methanol exhibit the structures capped on one side of the channel, whereas the compounds based on [3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methylphenyl]methanol induce an enlarged interaction interface that results in the open "face-back" tunnel through the PD-L1 dimer.

  • Organizational Affiliation

    Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland.

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
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
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
Query on 8J8

Download Ideal Coordinates CCD File 
E [auth B],
F [auth D]
C27 H32 N2 O4
Binding Affinity Annotations 
IDSourceBinding Affinity
8J8 BindingDB:  5N2D Kd: 1000 (nM) from 1 assay(s)
IC50: min: 1, max: 100 (nM) from 4 assay(s)
Binding MOAD:  5N2D IC50: 5.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.201α = 90
b = 85.734β = 90
c = 161.126γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science CenterPolandUMO-2012/06/A/ST5/00224
National Science CenterPolandUMO-2014/12/W/NZ1/00457
National Science CenterPolandUMO-2011/01/D/NZ1/01169
National Science CenterPolandUMO-2012/07/E/NZ1/01907
National Science CenterPolandUMO-2015/19/N/ST5/00347
National Science CenterPolandUMO-2016/20/T/NZ1/00519
National Science CenterPolandUMO-2015/19/D/NZ1/02009

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-26
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description