8P01 | pdb_00008p01

Crystal structure of human STING ectodomain in complex with BI 7446, a potent cyclic dinucleotide STING agonist with broad-spectrum variant activity for the treatment of cancer

• PDB DOI: https://doi.org/10.2210/pdb8P01/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2023-05-09 Released: 2023-07-26 
• Deposition Author(s): Nar, H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.262 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.240 (Depositor) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

Discovery of BI 7446: A Potent Cyclic Dinucleotide STING Agonist with Broad-Spectrum Variant Activity for the Treatment of Cancer.

Kuttruff, C.A., Fleck, M., Carotta, S., Arnhof, H., Bretschneider, T., Dahmann, G., Gremel, G., Grube, A., Handschuh, S., Heimann, A., Hofmann, M.H., Impagnatiello, M.A., Nar, H., Rast, G., Schaaf, O., Schmidt, E., Oost, T.

(2023) J Med Chem 66: 9376-9400

• PubMed: 37450324 
• DOI: https://doi.org/10.1021/acs.jmedchem.3c00510
• Primary Citation Related Structures: 
  8P01


• PubMed Abstract: 
  

  Activating the stimulator of interferon genes (STING) pathway with STING agonists is an attractive immune oncology concept to treat patients with tumors that are refractory to single-agent anti-PD-1 therapy. For best clinical translatability and broad application to cancer patients, STING agonists with potent cellular activation of all STING variants are desired. Novel cyclic dinucleotide (CDN)-based selective STING agonists were designed and synthesized comprising noncanonical nucleobase, ribose, and phosphorothioate moieties. This strategy led to the discovery of 2',3'-CDN 13 (BI 7446), which features unprecedented potency and activates all five STING variants in cellular assays. ADME profiling revealed that CDN 13 has attractive drug-like properties for development as an intratumoral agent. Injection of low doses of CDN 13 into tumors in mice induced long-lasting, tumor-specific immune-mediated tumor rejection. Based on its compelling preclinical profile, BI 7446 has been advanced to clinical trials (monotherapy and in combination with anti-PD-1 antibody).

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Organizational Affiliation: 
• Boehringer Ingelheim Pharma GmbH & Co. KG, 88400 Biberach an der Riss, Germany.
Boehringer Ingelheim RCV GmbH & Co KG, 1120 Vienna, Austria.

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

Macromolecule Content 

• Total Structure Weight: 29.04 kDa 
• Atom Count: 1,539 
• Modeled Residue Count: 181 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stimulator of interferon genes protein	A	248	Homo sapiens	Mutation(s): 0  Gene Names: STING1, ERIS, MITA, STING, TMEM173
UniProt & NIH Common Fund Data Resources
Find proteins for Q86WV6 (Homo sapiens) Explore Q86WV6  Go to UniProtKB:  Q86WV6
PHAROS:  Q86WV6 GTEx:  ENSG00000184584

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W78 (Subject of Investigation/LOI)	B [auth A]	3-[(1~{R},3~{R},6~{R},8~{R},9~{R},10~{R},12~{R},15~{R},17~{R},18~{R})-8-(6-aminopurin-9-yl)-9-fluoranyl-18-oxidanyl-3,12-bis(oxidanylidene)-3,12-bis(sulfanyl)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-yl]-6~{H}-imidazo[4,5-d]pyridazin-7-one C20 H22 F N9 O10 P2 S2 DAWAAQFAHQWLHI-UWLLIWRMSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
W78	BindingDB:  8P01	Kd: min: 1.5, max: 2.4 (nM) from 2 assay(s)
		EC50: min: 60, max: 5.00e+4 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.262 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.240 (Depositor) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.698	α = 90
b = 77.593	β = 98.08
c = 35.975	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
XDS	data reduction
autoPROC	data scaling
Aimless	data scaling
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-26 
Deposition Author(s): Nar, H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-07-26
  Type: Initial release
  
• Version 1.1: 2023-08-09
  Changes: Database references
• Version 1.2: 2024-06-19
  Changes: Data collection