MST3 in complex with compound MRIA9

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structure-Based Design of Selective Salt-Inducible Kinase Inhibitors.

Tesch, R.Rak, M.Raab, M.Berger, L.M.Kronenberger, T.Joerger, A.C.Berger, B.T.Abdi, I.Hanke, T.Poso, A.Strebhardt, K.Sanhaji, M.Knapp, S.

(2021) J Med Chem 64: 8142-8160

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c02144
  • Primary Citation of Related Structures:  
    7B30, 7B31, 7B32, 7B33, 7B34, 7B35, 7B36

  • PubMed Abstract: 

    Salt-inducible kinases (SIKs) are key metabolic regulators. The imbalance in SIK function is associated with the development of diverse cancers, including breast, gastric, and ovarian cancers. Chemical tools to clarify the roles of SIK in different diseases are, however, sparse and are generally characterized by poor kinome-wide selectivity. Here, we have adapted the pyrido[2,3- d ]pyrimidin-7-one-based p21-activated kinase (PAK) inhibitor G-5555 for the targeting of SIK, by exploiting differences in the back-pocket region of these kinases. Optimization was supported by high-resolution crystal structures of G-5555 bound to the known off-targets, MST3 and MST4, leading to a chemical probe, MRIA9, with dual SIK/PAK activity and excellent selectivity over other kinases. Furthermore, we show that MRIA9 sensitizes ovarian cancer cells to treatment with the mitotic agent paclitaxel, confirming earlier data from genetic knockdown studies and suggesting a combination therapy with SIK inhibitors and paclitaxel for the treatment of paclitaxel-resistant ovarian cancer.

  • Organizational Affiliation

    Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase 24306Homo sapiensMutation(s): 0 
Gene Names: STK24MST3STK3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6E0 (Homo sapiens)
Explore Q9Y6E0 
Go to UniProtKB:  Q9Y6E0
GTEx:  ENSG00000102572 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6E0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SQ8 (Subject of Investigation/LOI)
Query on SQ8

Download Ideal Coordinates CCD File 
B [auth A]1-[(5-azanyl-1,3-dioxan-2-yl)methyl]-3-[2-chloranyl-4-(3-fluoranylpyridin-2-yl)phenyl]-7-(methylamino)-1,6-naphthyridin-2-one
C25 H23 Cl F N5 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.429α = 90
b = 59.068β = 93.517
c = 61.728γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata processing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany397659447

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references
  • Version 1.2: 2021-07-07
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Database references, Refinement description