6R3K

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Terphenyl-Based Small-Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1 Protein-Protein Interaction.

Muszak, D.Surmiak, E.Plewka, J.Magiera-Mularz, K.Kocik-Krol, J.Musielak, B.Sala, D.Kitel, R.Stec, M.Weglarczyk, K.Siedlar, M.Domling, A.Skalniak, L.Holak, T.A.

(2021) J Med Chem 64: 11614-11636

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00957
  • Primary Citation of Related Structures:  
    6R3K, 7NLD

  • PubMed Abstract: 

    We describe a new class of potent PD-L1/PD-1 inhibitors based on a terphenyl scaffold that is derived from the rigidified biphenyl-inspired structure. Using in silico docking, we designed and then experimentally demonstrated the effectiveness of the terphenyl-based scaffolds in inhibiting PD-1/PD-L1 complex formation using various biophysical and biochemical techniques. We also present a high-resolution structure of the complex of PD-L1 with one of our most potent inhibitors to identify key PD-L1/inhibitor interactions at the molecular level. In addition, we show the efficacy of our most potent inhibitors in activating the antitumor response using primary human immune cells from healthy donors.


  • Organizational Affiliation

    Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 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
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JQT
Query on JQT

Download Ideal Coordinates CCD File 
F [auth B],
H [auth D]
(2~{S},4~{R})-1-[[5-chloranyl-2-[(3-cyanophenyl)methoxy]-4-[[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methyl-phenyl]methoxy]phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxylic acid
C36 H33 Cl N2 O7
QBXVXKRWOVBUDB-MVSFAKPFSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
G [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
JQT BindingDB:  6R3K IC50: 1.85 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.527α = 90
b = 84.609β = 90
c = 164.116γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland--
Polish National Science CentrePolandUMO-2012/06/A/ST5/00224
Polish National Science CentrePolandUMO-2014/12/W/NZ1/00457
Polish National Science CentrePolandUMO-2011/01/D/NZ1/01169
Polish National Science CentrePolandUMO-2012/07/E/NZ1/01907
Polish National Science CentrePoland2015/19/N/ST5/00347
Polish National Science CentrePolandUMO-2016/20/T/NZ1/00519
Polish National Science CentrePolandUMO-2015/19/D/NZ1/02009

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.2: 2021-08-25
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Refinement description