7X9Q | pdb_00007x9q

Crystal structure of human STING complexed with compound BSP16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.267 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of Selenium-Containing STING Agonists as Orally Available Antitumor Agents.

Feng, X.Pan, L.Qian, Z.Liu, D.Guan, X.Feng, L.Song, B.Xu, X.Tan, N.Ma, Y.Li, Z.Wang, Z.Bian, J.

(2022) J Med Chem 65: 15048-15065

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00634
  • Primary Citation Related Structures: 
    7X9Q

  • PubMed Abstract: 

    Activation of the stimulator of interferon genes (STING) pathway to achieve antitumor response is an attractive approach for cancer immunotherapy. In this study, we report the identification of BSP16 ( LF250 ) as a potent, orally available STING agonist. BSP16 strongly activates STING signaling in human and mouse cells and binds STING as a homodimer. A 2.4 Å cocrystal structure revealed that BSP16 could induce the "closed" conformation of STING. In vivo studies revealed that BSP16 is well tolerated, has an excellent pharmacokinetic profile as an oral drug, and induces tumor regression and durable antitumor immunity. The promising bioactivities of BSP16 make it valuable for further development as an antitumor agent.


  • Organizational Affiliation
    • State Key Laboratory of Natural Medicines, Department of Medicinal Chemistry, Department of TCMs Pharmaceuticals, China Pharmaceutical University, Nanjing 211100, P. R. China.

Macromolecule Content 

  • Total Structure Weight: 26.39 kDa 
  • Atom Count: 1,400 
  • Modeled Residue Count: 179 
  • Deposited Residue Count: 230 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Stimulator of interferon genes protein230Homo sapiensMutation(s): 0 
Gene Names: STING1
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
A9X
(Subject of Investigation/LOI)

Query on A9X



Download:Ideal Coordinates CCD File
B [auth A](2R)-4-(5,6-dimethoxy-1-benzoselenophen-2-yl)-2-ethyl-4-oxidanylidene-butanoic acid
C16 H18 O5 Se
BWQHPFYQJHFPHN-SECBINFHSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
A9X BindingDB:  7X9Q EC50: min: 5190, max: 1.00e+5 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.267 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.649α = 90
b = 54.502β = 98.4
c = 101.943γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31860245
National Natural Science Foundation of China (NSFC)China31960203
National Natural Science Foundation of China (NSFC)China82073702
National Natural Science Foundation of China (NSFC)China32070387
National Natural Science Foundation of China (NSFC)China81872746

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description