5NIX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Small-molecule inhibitors of PD-1/PD-L1 immune checkpoint alleviate the PD-L1-induced exhaustion of T-cells.

Skalniak, L.Zak, K.M.Guzik, K.Magiera, K.Musielak, B.Pachota, M.Szelazek, B.Kocik, J.Grudnik, P.Tomala, M.Krzanik, S.Pyrc, K.Domling, A.Dubin, G.Holak, T.A.

(2017) Oncotarget 8: 72167-72181

  • DOI: 10.18632/oncotarget.20050
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Antibodies targeting the PD-1/PD-L1 immune checkpoint achieved spectacular success in anticancer therapy in the recent years. In contrast, no small molecules with cellular activity have been reported so far. Here we provide evidence that small molecu ...

    Antibodies targeting the PD-1/PD-L1 immune checkpoint achieved spectacular success in anticancer therapy in the recent years. In contrast, no small molecules with cellular activity have been reported so far. Here we provide evidence that small molecules are capable of alleviating the PD-1/PD-L1 immune checkpoint-mediated exhaustion of Jurkat T-lymphocytes. The two optimized small-molecule inhibitors of the PD-1/PD-L1 interaction, BMS-1001 and BMS-1166, developed by Bristol-Myers Squibb, bind to human PD-L1 and block its interaction with PD-1, when tested on isolated proteins. The compounds present low toxicity towards tested cell lines and block the interaction of soluble PD-L1 with the cell surface-expressed PD-1. As a result, BMS-1001 and BMS-1166 alleviate the inhibitory effect of the soluble PD-L1 on the T-cell receptor-mediated activation of T-lymphocytes. Moreover, the compounds were effective in attenuating the inhibitory effect of the cell surface-associated PD-L1. We also determined the X-ray structures of the complexes of BMS-1001 and BMS-1166 with PD-L1, which revealed features that may be responsible for increased potency of the compounds compared to their predecessors. Further development may lead to the design of an anticancer therapy based on the orally delivered immune checkpoint inhibition.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Programmed cell death 1 ligand 1
A, B, C, D
128Homo sapiensMutation(s): 0 
Gene Names: CD274 (B7H1, PDCD1L1, PDCD1LG1, PDL1)
Find proteins for Q9NZQ7 (Homo sapiens)
Go to Gene View: CD274
Go to UniProtKB:  Q9NZQ7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
8YQ
Query on 8YQ

Download SDF File 
Download CCD File 
A, D
(2~{R},3~{R},5~{R})-2-[[2-[[3-(aminomethyl)phenyl]methoxy]-4-[[3-(1,4-benzodioxin-6-yl)-2-methyl-phenyl]methoxy]-5-chloranyl-phenyl]methyl]-5-oxidanyl-pyrrolidine-3-carboxylic acid
C36 H35 Cl N2 O7
YRYUBNOJILTDAA-GMBIYBECSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.527α = 90.00
b = 84.609β = 90.00
c = 164.116γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science CenterPoland--
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 CenterPoland2015/19/N/ST5/00347
National Science CenterPolandUMO-2016/20/T/NZ1/00519
National Science CenterPolandUMO-2015/19/D/NZ1/02009

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Advisory, Data collection, Derived calculations