6XF4

Crystal structure of STING REF variant in complex with E7766

PDB DOI: https://doi.org/10.2210/pdb6XF4/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free: 0.271
R-Value Work: 0.221
R-Value Observed: 0.224

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 44.28 kDa
Atom Count: 3,002
Modelled Residue Count: 351
Deposited Residue Count: 378
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stimulator of interferon genes protein	A, B	189	Homo sapiens	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q86WV6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
V5V (Subject of Investigation/LOI) Query on V5V Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	D [auth A] E [auth A] F [auth B] G [auth B] H [auth B] D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free: 0.271
R-Value Work: 0.221
R-Value Observed: 0.224
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.733	α = 90
b = 77.831	β = 90
c = 131.689	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-02-17

Deposition Author(s):

Chen, Y.

Wang, J.Y.

Kim, D.-S.

Revision History (Full details and data files)

Version 1.0: 2021-02-17
Type: Initial release
Version 1.1: 2021-06-16
Changes: Database references
Version 1.2: 2024-03-06
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-04-03
Changes: Refinement description