6XF3 | pdb_00006xf3

Crystal structure of STING in complex with E7766

• PDB DOI: https://doi.org/10.2210/pdb6XF3/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-06-15 Released: 2021-02-17 
• Deposition Author(s): Chen, Y., Wang, J.Y., Kim, D.-S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

E7766, a Macrocycle-Bridged Stimulator of Interferon Genes (STING) Agonist with Potent Pan-Genotypic Activity.

Kim, D.S., Endo, A., Fang, F.G., Huang, K.C., Bao, X., Choi, H.W., Majumder, U., Shen, Y.Y., Mathieu, S., Zhu, X., Sanders, K., Noland, T., Hao, M.H., Chen, Y., Wang, J.Y., Yasui, S., TenDyke, K., Wu, J., Ingersoll, C., Loiacono, K.A., Hutz, J.E., Sarwar, N.

(2021) ChemMedChem 16: 1740-1743

• PubMed: 33522135 
• DOI: https://doi.org/10.1002/cmdc.202100068
• Primary Citation of Related Structures:  
  6XF3, 6XF4


• PubMed Abstract: 
  

  A strategy for creating potent and pan-genotypic stimulator of interferon genes (STING) agonists is described. Locking a bioactive U-shaped conformation of cyclic dinucleotides by introducing a transannular macrocyclic bridge between the nucleic acid bases leads to a topologically novel macrocycle-bridged STING agonist (MBSA). In addition to substantially enhanced potency, the newly designed MBSAs, exemplified by clinical candidate E7766, exhibit broad pan-genotypic activity in all major human STING variants. E7766 is shown to have potent antitumor activity with long lasting immune memory response in a mouse liver metastatic tumor model. Two complementary stereoselective synthetic routes to E7766 are also described.

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Organizational Affiliation: 

Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA.

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)

Macromolecule Content

• Total Structure Weight: 43.95 kDa 
• Atom Count: 3,159 
• Modelled Residue Count: 349 
• Deposited Residue Count: 378 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stimulator of interferon genes protein	A, B	189	Homo sapiens	Mutation(s): 1  Gene Names: STING1, ERIS, MITA, 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
V5V (Subject of Investigation/LOI)	C [auth A]	(1R,3R,15E,28R,29R,30R,31R,34R,36R,39S,41R)-29,41-difluoro-34,39-disulfanyl-2,33,35,38,40,42-hexaoxa-4,6,9,11,13,18,20,22,25,27-decaaza-34,39-diphosphaoctacyclo[28.6.4.1~3,36~.1~28,31~.0~4,8~.0~7,12~.0~19,24~.0~23,27~]dotetraconta-5,7,9,11,15,19,21,23,25-nonaene 34,39-dioxide (non-preferred name) C24 H26 F2 N10 O8 P2 S2 YQSAUMRQALUWNS-VUCARUFASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.82	α = 90
b = 78.11	β = 90
c = 132.212	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PHASER	phasing
Coot	model building
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Chen, Y., Wang, J.Y., Kim, D.-S.

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2021-06-16
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description