7Q85

Crystal structure of human STING in complex with MD1193


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Vinylphosphonate-based cyclic dinucleotides enhance STING-mediated cancer immunotherapy.

Dejmek, M.Brazdova, A.Otava, T.Polidarova, M.P.Klima, M.Smola, M.Vavrina, Z.Budesinsky, M.Dracinsky, M.Liboska, R.Boura, E.Birkus, G.Nencka, R.

(2023) Eur J Med Chem 259: 115685-115685

  • DOI: https://doi.org/10.1016/j.ejmech.2023.115685
  • Primary Citation of Related Structures:  
    7Q85

  • PubMed Abstract: 

    Cyclic dinucleotides (CDNs) trigger the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway, which plays a key role in cytosolic DNA sensing and thus in immunomodulation against infections, cell damage and cancer. However, cancer immunotherapy trials with CDNs have shown immune activation, but not complete tumor regression. Nevertheless, we designed a novel class of CDNs containing vinylphosphonate based on a STING-affinity screening assay. In vitro, acyloxymethyl phosphate/phosphonate prodrugs of these vinylphosphonate CDNs were up to 1000-fold more potent than the clinical candidate ADU-S100. In vivo, the lead prodrug induced tumor-specific T cell priming and facilitated tumor regression in the 4T1 syngeneic mouse model of breast cancer. Moreover, we solved the crystal structure of this ligand bound to the STING protein. Therefore, our findings not only validate the therapeutic potential of vinylphosphonate CDNs but also open up opportunities for drug development in cancer immunotherapy bridging innate and adaptive immunity.


  • Organizational Affiliation

    Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 6, 166 10, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Stimulator of interferon genes protein204Homo sapiensMutation(s): 1 
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
98F (Subject of Investigation/LOI)
Query on 98F

Download Ideal Coordinates CCD File 
B [auth A]9-[(1R,6R,8R,13E,15R,17R,18R)-17-(6-aminopurin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,16-pentaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadec-13-en-8-yl]purin-6-amine
C21 H22 F2 N10 O9 P2
ZKWIHCLAWIBCNH-FAOXOZTKSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.034α = 90
b = 111.034β = 90
c = 35.091γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2023-05-31
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2023-08-23
    Changes: Data collection, Database references
  • Version 1.3: 2024-02-07
    Changes: Refinement description