9QVT | pdb_00009qvt

Crystal structure of STING CTD in complex with potent agonist D5

• PDB DOI: https://doi.org/10.2210/pdb9QVT/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-04-11 Released: 2025-09-24 
• Deposition Author(s): dos Reis, C.V., Hsu, N.-S., Rooney, T., Skidmore, J., Bernardes, G.J.L., Hyvonen, M.
• Funding Organization(s): Alzheimers Research UK (ARUK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 
  0.388 (Depositor), 0.392 (DCC) 
• R-Value Work: 
  0.342 (Depositor), 0.337 (DCC) 

Starting Model: experimental

Literature

Tumour-specific STING agonist synthesis via a two-component prodrug system.

Hsu, N.S., Tang, C., Mendes, R.V., Labao-Almeida, C., Dos Reis, C.V., Coelho, A.R., Marques, M.C., Cabeza Cabrerizo, M., Misteli, R., Rooney, T.P.C., Hyvonen, M., Corzana, F., Fior, R., Bernardes, G.J.L.

(2025) Nat Chem 17: 1941-1951

• PubMed: 40957952 
• DOI: https://doi.org/10.1038/s41557-025-01930-9
• Primary Citation Related Structures: 
  9QVT


• PubMed Abstract: 
  

  Pharmacological activation of STING holds promise in cancer treatment. A recent trend is the development of tumour-specific or conditionally activated STING agonists for enhanced safety and efficacy. Here we explore an unconventional prodrug activation strategy for on-tumour synthesis of a potent agonist. Leveraging the unique mechanism of MSA2, a small-molecule agonist that dimerizes non-covalently before binding to STING, we showed that its analogues bearing reactive functional groups readily and selectively form covalent dimers under mild conditions and in complex environments. We identified a reacting pair that led to a thioether-linked dimer with submicromolar potency in cell-based assays. Caging one of the reactants with a self-immolative β-glucuronide moiety resulted in a two-component prodrug system that near-exclusively formed the active compounds in tumours overexpressing β-glucuronidase. These results exemplify the use of small-molecule recognition for on-site generation of active compounds from benign precursors.

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Organizational Affiliation: 
• Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
GIMM - Gulbenkian Institute for Molecular Medicine, Lisbon, Portugal.
Xi'an Fengcheng Hospital, Xi'an, China.
Champalimaud Research, Champalimaud Foundation, Lisbon, Portugal.
The ALBORADA Drug Discovery Institute, University of Cambridge, Cambridge, UK.
Department of Biochemistry, University of Cambridge, Cambridge, UK.
The Discovery Centre, Cambridge, UK.
Departamento de Química and Instituto de Investigación en Química de la Universidad de La Rioja (IQUR), Universidad de La Rioja, Logroño, Spain.
Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK. [e-mail].
GIMM - Gulbenkian Institute for Molecular Medicine, Lisbon, Portugal. [e-mail].
Translational Chemical Biology Group, Spanish National Cancer Research Centre, Madrid, Spain. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 27.76 kDa 
• Atom Count: 1,349 
• Modeled Residue Count: 182 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stimulator of interferon genes protein	A	242	Homo sapiens	Mutation(s): 2  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
A1JA0 (Subject of Investigation/LOI)	B [auth A]	4-[6-methoxy-5-[[6-methoxy-2-(4-oxidanyl-4-oxidanylidene-butanoyl)-1-benzothiophen-5-yl]sulfanylmethylsulfanyl]-1-benzothiophen-2-yl]-4-oxidanylidene-butanoic acid C27 H24 O8 S4 NGJBOFBFUVNHEM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free:  0.388 (Depositor), 0.392 (DCC) 
• R-Value Work:  0.342 (Depositor), 0.337 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.681	α = 90
b = 75.595	β = 97.75
c = 34.138	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
Aimless	data scaling
BUSTER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): dos Reis, C.V., Hsu, N.-S., Rooney, T., Skidmore, J., Bernardes, G.J.L., Hyvonen, M.

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Funding Organization	Location	Grant Number
Alzheimers Research UK (ARUK)	United Kingdom	ARUK-2015DDI-CAM

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release
  
• Version 1.1: 2025-12-10
  Changes: Database references