Crystal structure of human STING (G230A, H232R, R293Q) in complex with Compound 1

Experimental Data Snapshot

  • Resolution: 1.36 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

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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

  • 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.

  • 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Stimulator of interferon genes protein
A, B
188Homo sapiensMutation(s): 3 
UniProt & NIH Common Fund Data Resources
Find proteins for Q86WV6 (Homo sapiens)
Explore Q86WV6 
Go to UniProtKB:  Q86WV6
GTEx:  ENSG00000184584 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86WV6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K5P (Subject of Investigation/LOI)
Query on K5P

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(3S,4S)-2-(4-tert-butylphenyl)-3-(4-methoxyphenyl)-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxylic acid
C27 H27 N O4
Query on CA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.36 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.2α = 90
b = 77.71β = 90
c = 125.41γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
AutoPROCdata processing
XDSdata processing

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

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