5O4Y

Structure of human PD-L1 in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Bioactive Macrocyclic Inhibitors of the PD-1/PD-L1 Immune Checkpoint.

Magiera-Mularz, K.Skalniak, L.Zak, K.M.Musielak, B.Rudzinska-Szostak, E.Kocik, J.Grudnik, P.Sala, D.Zarganes-Tzitzikas, T.Shaabani, S.Domling, A.Dubin, G.Holak, T.A.

(2017) Angew. Chem. Int. Ed. Engl. 56: 13732-13735

  • DOI: 10.1002/anie.201707707
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Blockade of the immunoinhibitory PD-1/PD-L1 pathway using monoclonal antibodies has shown impressive results with durable clinical antitumor responses. Anti-PD-1 and anti-PD-L1 antibodies have now been approved for the treatment of a number of tumor ...

    Blockade of the immunoinhibitory PD-1/PD-L1 pathway using monoclonal antibodies has shown impressive results with durable clinical antitumor responses. Anti-PD-1 and anti-PD-L1 antibodies have now been approved for the treatment of a number of tumor types, whereas the development of small molecules targeting immune checkpoints lags far behind. We characterized two classes of macrocyclic-peptide inhibitors directed at the PD-1/PD-L1 pathway. We show that these macrocyclic compounds act by directly binding to PD-L1 and that they are capable of antagonizing PD-L1 signaling and, similarly to antibodies, can restore the function of T-cells. We also provide the crystal structures of two of these small-molecule inhibitors bound to PD-L1. The structures provide a rationale for the checkpoint inhibition by these small molecules, and a description of their small molecule/PD-L1 interfaces provides a blueprint for the design of small-molecule inhibitors of the PD-1/PD-L1 pathway.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Programmed cell death 1 ligand 1
B, C, E
118Homo 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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PHE-MAA-ASN-PRO-HIS-LEU-SER-TRP-SER-TRP-9KK-9KK-ARG-CCS-GLY-NH2
A, D, F
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
CCS
Query on CCS
A, D, F
L-PEPTIDE LINKINGC5 H9 N O4 SCYS
NH2
Query on NH2
A, D, F
NON-POLYMERH2 N

--

9KK
Query on 9KK
A, D, F
L-peptide linkingC7 H15 N O2

--

MAA
Query on MAA
A, D, F
L-peptide linkingC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.550α = 90.00
b = 80.950β = 104.49
c = 54.230γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science CenterPolandUMO-2014/12/W/NZ1/00457
National Science CenterPolandUMO-2012/07/E/NZ1/01907
European UnionPolandMarie Curie FP7-Reintegration-Grant

Revision History 

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2017-10-25
    Type: Database references