7B33

MST3 in complex with MRIA11

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

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: 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 ...

    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: 

    German Translational Cancer Network (DKTK) and Frankfurt Cancer Institute (FCI), Frankfurt am Main 60438, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase 24A306Homo sapiensMutation(s): 0 
Gene Names: STK24, MST3, STK3
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6E0 (Homo sapiens)
Explore Q9Y6E0 
Go to UniProtKB:  Q9Y6E0
PHAROS:  Q9Y6E0
GTEx:  ENSG00000102572
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SQE (Subject of Investigation/LOI)
Query on SQE
Download Ideal Coordinates CCD File 
F [auth A]8-[(5-azanyl-1,3-dioxan-2-yl)methyl]-6-[4-[6-[bis(fluoranyl)methyl]pyridin-2-yl]-2-chloranyl-phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7-one
C25 H23 Cl F2 N6 O3
SPTBMDXMZIQSLW-WEHONNDLSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A], E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.972α = 90
b = 58.954β = 93.128
c = 61.441γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  


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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