9PPL | pdb_00009ppl

Structure of STING in complex with MK-2118


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.186 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of MK-2118, a Small-Molecule Agonist of STING.

Henderson, T.Altman, M.D.Buevich, A.V.Cash, B.Cemerski, S.Chang, W.Chen, Y.Childers, M.Cumming, J.Dandliker, P.J.Feng, G.Haidle, A.Hayes, R.P.Ho, T.Jewell, J.P.Kariv, I.Knemeyer, I.Kopinja, J.Lacey, B.M.Laskey, J.Lesburg, C.A.Liang, R.Lim, J.Long, B.J.Lu, M.Ma, Y.Minnihan, E.C.Otte, R.D.O'Donnell, G.Pan, B.S.Perera, S.A.Piesvaux, J.A.Presland, J.P.Price, L.Rakhilina, L.Sauvagnat, B.Schroeder, G.K.Sharma, S.Trotter, B.W.Tyagarajan, S.Woo, H.Wyss, D.F.Xu, S.Addona, G.H.Bennett, D.J.

(2026) ACS Med Chem Lett 17: 1501-1507

  • DOI: https://doi.org/10.1021/acsmedchemlett.5c00540
  • Primary Citation Related Structures: 
    9PPL

  • PubMed Abstract: 

    Agonists of Stimulator of Interferon Genes (STING) have the potential to activate the innate and adaptive immune system for cancer treatment. Early efforts in identifying suitable therapeutics were focused on cyclic dinucleotide (CDN) analogs of 2',3'-cGAMP, the endogenous ligand to STING. CDNs lack of tractable bioavailability led us to consider small-molecule modulators of STING. We previously reported the identification of MSA-2, an orally available non-nucleotide STING agonist with antitumor activity. Optimization efforts in this series faced challenges with uniform activity across species, cell shift, and steep structure activity relationships. Herein we report lead optimization efforts guided by structure-based drug design to identify the MSA-2 analog MK-2118.


  • Organizational Affiliation
    • †Department of Discovery Chemistry; ‡Department of Quantitative Biosciences; §Department of Discovery Oncology; ∥Department of Pharmacokinetics; ⊥Department of Discovery Pharmaceutical Sciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States.

Macromolecule Content 

  • Total Structure Weight: 21.86 kDa 
  • Atom Count: 1,555 
  • Modeled Residue Count: 179 
  • Deposited Residue Count: 188 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Stimulator of interferon genes protein188Homo sapiensMutation(s): 2 
Gene Names: STING1ERISMITATMEM173
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CIY
(Subject of Investigation/LOI)

Query on A1CIY



Download:Ideal Coordinates CCD File
B [auth A](2S)-4-(5,6-dimethoxy-1-benzothiophen-2-yl)-2-methyl-4-oxobutanoic acid
C15 H16 O5 S
WBHPMBQELUEIIV-QMMMGPOBSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.186 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.08α = 90
b = 78.08β = 97.22
c = 36.47γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-01
    Type: Initial release
  • Version 1.1: 2026-07-29
    Changes: Database references