9QVT | pdb_00009qvt

Crystal structure of STING CTD in complex with potent agonist D5


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
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41557-025-01930-9
  • Primary Citation of 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.


  • Organizational Affiliation
    • Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Stimulator of interferon genes protein242Homo sapiensMutation(s): 2 
Gene Names: STING1ERISMITASTINGTMEM173
UniProt & NIH Common Fund Data Resources
Find proteins for Q86WV6 (Homo sapiens)
Explore Q86WV6 
Go to UniProtKB:  Q86WV6
PHAROS:  Q86WV6
GTEx:  ENSG00000184584 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86WV6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JA0 (Subject of Investigation/LOI)
Query on A1JA0

Download Ideal Coordinates CCD File 
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 = 89.681α = 90
b = 75.595β = 97.75
c = 34.138γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Alzheimers Research UK (ARUK)United KingdomARUK-2015DDI-CAM

Revision History  (Full details and data files)

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