Crystal structure of STK4 (MST1) in complex with compound 6

Experimental Data Snapshot

  • Resolution: 2.58 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

Starting Model: experimental
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Inhibitors of the Hippo Pathway Kinases STK3/MST2 and STK4/MST1 Have Utility for the Treatment of Acute Myeloid Leukemia.

Bata, N.Chaikuad, A.Bakas, N.A.Limpert, A.S.Lambert, L.J.Sheffler, D.J.Berger, L.M.Liu, G.Yuan, C.Wang, L.Peng, Y.Dong, J.Celeridad, M.Layng, F.Knapp, S.Cosford, N.D.P.

(2022) J Med Chem 65: 1352-1369

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00804
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Serine/threonine-protein kinases 3 and 4 (STK3 and STK4, respectively) are key components of the Hippo signaling pathway, which regulates cell proliferation and death and provides a potential therapeutic target for acute myeloid leukemia (AML). Herein, we report the structure-based design of a series of pyrrolopyrimidine derivatives as STK3 and STK4 inhibitors. In an initial screen, the compounds exhibited low nanomolar potency against both STK3 and STK4. Crystallization of compound 6 with STK4 revealed two-point hinge binding in the ATP-binding pocket. Further characterization and analysis demonstrated that compound 20 (SBP-3264) specifically inhibited the Hippo signaling pathway in cultured mammalian cells and possessed favorable pharmacokinetic and pharmacodynamic properties in mice. We show that genetic knockdown and pharmacological inhibition of STK3 and STK4 suppress the proliferation of AML cells in vitro. Thus, SBP-3264 is a valuable chemical probe for understanding the roles of STK3 and STK4 in AML and is a promising candidate for further advancement as a potential therapy.

  • Organizational Affiliation

    Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase 4
A, B
314Homo sapiensMutation(s): 0 
Gene Names: STK4KRS2MST1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13043 (Homo sapiens)
Explore Q13043 
Go to UniProtKB:  Q13043
PHAROS:  Q13043
GTEx:  ENSG00000101109 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13043
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OJ5 (Subject of Investigation/LOI)
Query on OJ5

Download Ideal Coordinates CCD File 
K [auth A],
L [auth B]
C16 H15 Cl N4 O
Query on 3FX

Download Ideal Coordinates CCD File 
C [auth A](2R)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid
C9 H19 N O4 S
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
C3 H8 O3
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on TPO
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.58 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.68α = 90
b = 111.68β = 90
c = 171.486γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2021-12-08
    Changes: Database references
  • Version 1.2: 2022-02-09
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Refinement description