6MX0

Crystal structure of human STING apoprotein (G230A, H232R, R293Q)

• PDB DOI:  https://doi.org/10.2210/pdb6MX0/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-10-30 Released: 2018-12-19 
• Deposition Author(s): Lesburg, C.A., Siu, T., Ho, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.220 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Literature

Discovery of a Novel cGAMP Competitive Ligand of the Inactive Form of STING.

Siu, T., Altman, M.D., Baltus, G.A., Childers, M., Ellis, J.M., Gunaydin, H., Hatch, H., Ho, T., Jewell, J., Lacey, B.M., Lesburg, C.A., Pan, B.S., Sauvagnat, B., Schroeder, G.K., Xu, S.

(2019) ACS Med Chem Lett 10: 92-97

• PubMed: 30655953 
• DOI: https://doi.org/10.1021/acsmedchemlett.8b00466
• Primary Citation of Related Structures:  
  6MX0, 6MX3, 6MXE


• PubMed Abstract: 
  

Drugging large protein pockets is a challenge due to the need for higher molecular weight ligands, which generally possess undesirable physicochemical properties. In this communication, we highlight a strategy leveraging small molecule active site dimers to inhibit the large symmetric binding pocket in the STING protein. By taking advantage of the 2:1 binding stoichiometry, maximal buried interaction with STING protein can be achieved while maintaining the ligand physicochemical properties necessary for oral exposure. This mode of binding requires unique considerations for potency optimization including simultaneous optimization of protein-ligand as well as ligand-ligand interactions. Successful implementation of this strategy led to the identification of 18 , which exhibits good oral exposure, slow binding kinetics, and functional inhibition of STING-mediated cytokine release.

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Organizational Affiliation: 

Departments of Chemistry, Immunology, Chemistry Modeling and Informatics, In Vitro Pharmacology, Target Protein Design and Structural Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 43.1 kDa 
• Atom Count: 2,992 
• Modelled Residue Count: 340 
• Deposited Residue Count: 376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stimulator of interferon genes protein	A, B	188	Homo sapiens	Mutation(s): 3  Gene Names: TMEM173, ERIS, MITA, STING, STING1
UniProt & NIH Common Fund Data Resources
Find proteins for Q86WV6 (Homo sapiens) Explore Q86WV6  Go to UniProtKB:  Q86WV6
PHAROS:  Q86WV6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.220 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.47	α = 90
b = 77.46	β = 90
c = 126.58	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
AutoPROC	data reduction
XDS	data reduction
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-19 
Deposition Author(s): Lesburg, C.A., Siu, T., Ho, T.

Revision History  

• Version 1.0: 2018-12-19
  Type: Initial release
  
• Version 1.1: 2019-01-30
  Changes: Data collection, Database references