7KVX

Structure of hSTING in complex with novel carbocyclic pyrimidine CDN 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Identification of Novel Carbocyclic Pyrimidine Cyclic Dinucleotide STING Agonists for Antitumor Immunotherapy Using Systemic Intravenous Route.

Vyskocil, S.Cardin, D.Ciavarri, J.Conlon, J.Cullis, C.England, D.Gershman, R.Gigstad, K.Gipson, K.Gould, A.Greenspan, P.Griffin, R.Gulavita, N.Harrison, S.Hu, Z.Hu, Y.Hata, A.Huang, J.Huang, S.C.Janowick, D.Jones, M.Kolev, V.Langston, S.P.Lee, H.M.Li, G.Lok, D.Ma, L.Mai, D.Malley, J.Matsuda, A.Mizutani, H.Mizutani, M.Molchanova, N.Nunes, E.Pusalkar, S.Renou, C.Rowland, S.Sato, Y.Shaw, M.Shen, L.Shi, Z.Skene, R.Soucy, F.Stroud, S.Xu, H.Xu, T.Abu-Yousif, A.O.Zhang, J.

(2021) J Med Chem 64: 6902-6923

  • DOI: 10.1021/acs.jmedchem.1c00374
  • Primary Citation of Related Structures:  
    7KVX, 7KVZ, 7KW1

  • PubMed Abstract: 
  • Stimulator of Interferon Genes (STING) plays an important role in innate immunity by inducing type I interferon production upon infection with intracellular pathogens. STING activation can promote increased T-cell activation and inflammation in the tumor microenvironment, resulting in antitumor immunity ...

    Stimulator of Interferon Genes (STING) plays an important role in innate immunity by inducing type I interferon production upon infection with intracellular pathogens. STING activation can promote increased T-cell activation and inflammation in the tumor microenvironment, resulting in antitumor immunity. Natural and synthetic cyclic dinucleotides (CDNs) are known to activate STING, and several synthetic CDN molecules are being investigated in the clinic using an intratumoral administration route. Here, we describe the identification of STING agonist 15a , a cyclic dinucleotide structurally diversified from natural ligands with optimized properties for systemic intravenous (iv) administration. Our studies have shown that STING activation by 15a leads to an acute innate immune response as measured by cytokine secretion and adaptive immune response via activation of CD8+ cytotoxic T-cells, which ultimately provides robust antitumor efficacy.


    Organizational Affiliation

    Drug Discovery Sciences, Takeda Pharmaceuticals International Company, 9625 Towne Centre Drive, San Diego, California 92121, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Stimulator of interferon genes proteinA243Homo sapiensMutation(s): 0 
Gene Names: STINGLOC340061hCG_1782396STING1ERISMITATMEM173
UniProt & NIH Common Fund Data Resources
Find proteins for Q86WV6 (Homo sapiens)
Explore Q86WV6 
Go to UniProtKB:  Q86WV6
PHAROS:  Q86WV6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86WV6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
X5J (Subject of Investigation/LOI)
Query on X5J

Download Ideal Coordinates CCD File 
B [auth A](2R,5R,7R,8R,10R,12aR,14R,15aS,16R)-7-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-16-hydroxy-14-[(pyrimidin-4-yl)amino]-2,10-disulfanyldecahydro-2H,10H-5,8-methano-2lambda~5~,10lambda~5~-cyclopenta[l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecine-2,10-dione
C20 H26 N8 O9 P2 S2
DXJHOSYLPZBMEZ-FEFYGENMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.495α = 90
b = 78.539β = 96.52
c = 36.01γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-06-02 
  • Deposition Author(s): Skene, R.

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release
  • Version 1.1: 2021-06-09
    Changes: Database references