5J89 | pdb_00005j89

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

• PDB DOI: https://doi.org/10.2210/pdb5J89/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-04-07 Released: 2016-04-27 
• Deposition Author(s): Zak, K.M., Grudnik, P., Guzik, K., Zieba, B.J., Musielak, B., Doemling, P., Dubin, G., Holak, T.A.
• Funding Organization(s): European Commissiona, National Science Centre, European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.256 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.202 (Depositor) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

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

• PubMed: 27083005 
• DOI: https://doi.org/10.18632/oncotarget.8730
• Primary Citation Related Structures: 
  5J89, 5J8O


• 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 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.

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Organizational Affiliation: 
• Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa, Krakow, Poland.
Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa, Krakow, Poland.
Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena, Krakow, Poland.
Department for Drug Design, University of Groningen, A. Deusinglaan , Groningen, The Netherlands.
Max Planck Institute for Biochemistry, Am Klopferspitz, Martinsried, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 67.84 kDa 
• Atom Count: 4,122 
• Modeled Residue Count: 501 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death 1 ligand 1	A [auth C], B [auth A], C [auth D], D [auth B]	144	Homo sapiens	Mutation(s): 0  Gene Names: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZQ7 (Homo sapiens) Explore Q9NZQ7  Go to UniProtKB:  Q9NZQ7
PHAROS:  Q9NZQ7 GTEx:  ENSG00000120217

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6GX	E [auth C], G [auth B]	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
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.256 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.202 (Depositor) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.834	α = 90
b = 85.093	β = 90
c = 161.772	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-04-27 
Deposition Author(s): Zak, K.M., Grudnik, P., Guzik, K., Zieba, B.J., Musielak, B., Doemling, P., Dubin, G., Holak, T.A.

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Funding Organization	Location	Grant Number
European Commissiona	Poland	Marie Curie FP7-Reintegration-Grant
National Science Centre	Poland	UMO-2012/06/A/ST5/00224
National Science Centre	Poland	UMO-2011/01/D/NZ1/01169
European Union	Poland	POIG.02.01.00-12-064/08
European Union	Poland	POIG.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
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary