5J89

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: 0.256 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for small molecule targeting of the programmed death ligand 1 (PD-L1).

Zak, K.M.Grudnik, P.Guzik, K.Zieba, B.J.Musielak, B.Domling, A.Dubin, G.Holak, T.A.

(2016) Oncotarget 7: 30323-30335

  • DOI: 10.18632/oncotarget.8730
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Targeting the PD-1/PD-L1 immunologic checkpoint with monoclonal antibodies has provided unprecedented results in cancer treatment in the recent years. Development of chemical inhibitors for this pathway lags the antibody development because of insuff ...

    Targeting the PD-1/PD-L1 immunologic checkpoint with monoclonal antibodies has provided unprecedented results in cancer treatment in the recent years. Development of chemical inhibitors for this pathway lags the antibody development because of insufficient structural information. The first nonpeptidic chemical inhibitors that target the PD-1/PD-L1 interaction have only been recently disclosed by Bristol-Myers Squibb. Here, we show that these small-molecule compounds bind directly to PD-L1 and that they potently block PD-1 binding. Structural studies reveal a dimeric protein complex with a single small molecule which stabilizes the dimer thus occluding the PD-1 interaction surface of PD-L1s. The small-molecule interaction "hot spots" on PD-L1 surfaces suggest approaches for the PD-1/PD-L1 antagonist drug discovery.


    Organizational Affiliation

    Max Planck Institute for Biochemistry, Am Klopferspitz, Martinsried, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Programmed cell death 1 ligand 1
A, B, C, D
144Homo sapiensMutation(s): 0 
Gene Names: CD274B7H1PDCD1L1PDCD1LG1PDL1
Find proteins for Q9NZQ7 (Homo sapiens)
Go to UniProtKB:  Q9NZQ7
NIH Common Fund Data Resources
PHAROS  Q9NZQ7
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6GX
Query on 6GX

Download CCD File 
B, C
N-{2-[({2-methoxy-6-[(2-methyl[1,1'-biphenyl]-3-yl)methoxy]pyridin-3-yl}methyl)amino]ethyl}acetamide
C25 H29 N3 O3
JEDPSOYOYVELLZ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.834α = 90
b = 85.093β = 90
c = 161.772γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionaPolandMarie Curie FP7-Reintegration-Grant
National Science CentrePolandUMO-2012/06/A/ST5/00224
National Science CentrePolandUMO-2011/01/D/NZ1/01169
European UnionPolandPOIG.02.01.00-12-064/08
European UnionPolandPOIG.02.01.00-12-167/08

Revision History 

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-09-14
    Changes: Database references