5N2D

Structure of PD-L1/small-molecule inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.267 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 8J8Click on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

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.


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
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8J8
Query on 8J8

Download Ideal Coordinates CCD File 
E [auth B],
F [auth D]
~{N}-[2-[[2,6-dimethoxy-4-[(2-methyl-3-phenyl-phenyl)methoxy]phenyl]methylamino]ethyl]ethanamide
C27 H32 N2 O4
OYNIISWIMDFFAF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
8J8 BindingDB:  5N2D Kd: 1000 (nM) from 1 assay(s)
IC50: min: 1, max: 100 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
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
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 8J8Click on this verticalbar to view details

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
  • Version 1.3: 2024-10-16
    Changes: Structure summary