6VQN | pdb_00006vqn

Co-crystal structure of human PD-L1 complexed with Compound A

• PDB DOI: https://doi.org/10.2210/pdb6VQN/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-02-05 Released: 2021-01-20 
• Deposition Author(s): White, A., Lakshminarasimhan, D., Leo, C., Suto, R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.228 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Checkpoint inhibition through small molecule-induced internalization of programmed death-ligand 1.

Park, J.J., Thi, E.P., Carpio, V.H., Bi, Y., Cole, A.G., Dorsey, B.D., Fan, K., Harasym, T., Iott, C.L., Kadhim, S., Kim, J.H., Lee, A.C.H., Nguyen, D., Paratala, B.S., Qiu, R., White, A., Lakshminarasimhan, D., Leo, C., Suto, R.K., Rijnbrand, R., Tang, S., Sofia, M.J., Moore, C.B.

(2021) Nat Commun 12: 1222-1222

• PubMed: 33619272 
• DOI: https://doi.org/10.1038/s41467-021-21410-1
• Primary Citation Related Structures: 
  6VQN


• PubMed Abstract: 
  

  Programmed death-ligand 1 is a glycoprotein expressed on antigen presenting cells, hepatocytes, and tumors which upon interaction with programmed death-1, results in inhibition of antigen-specific T cell responses. Here, we report a mechanism of inhibiting programmed death-ligand 1 through small molecule-induced dimerization and internalization. This represents a mechanism of checkpoint inhibition, which differentiates from anti-programmed death-ligand 1 antibodies which function through molecular disruption of the programmed death 1 interaction. Testing of programmed death ligand 1 small molecule inhibition in a humanized mouse model of colorectal cancer results in a significant reduction in tumor size and promotes T cell proliferation. In addition, antigen-specific T and B cell responses from patients with chronic hepatitis B infection are significantly elevated upon programmed death ligand 1 small molecule inhibitor treatment. Taken together, these data identify a mechanism of small molecule-induced programmed death ligand 1 internalization with potential therapeutic implications in oncology and chronic viral infections.

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Organizational Affiliation: 
• Arbutus Biopharma Inc, Warminster, PA, USA.
Xtal BioStructures Inc., Natick, MA, USA.
Arbutus Biopharma Inc, Warminster, PA, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 45.57 kDa 
• Atom Count: 3,114 
• Modeled Residue Count: 365 
• Deposited Residue Count: 387 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death 1 ligand 1	A, B, C	129	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R81 (Subject of Investigation/LOI)	D [auth B], E [auth C]	N,N'-(2,2'-dimethyl[1,1'-biphenyl]-3,3'-diyl)bis(5-{[(2-hydroxyethyl)amino]methyl}pyridine-2-carboxamide) C32 H36 N6 O4 FZEPAZRIEAMJFE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.228 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.003	α = 90
b = 172.173	β = 90
c = 80.585	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-20 
Deposition Author(s): White, A., Lakshminarasimhan, D., Leo, C., Suto, R.K.

Revision History  

• Version 1.0: 2021-01-20
  Type: Initial release
  
• Version 1.1: 2021-03-10
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary