Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.57 kDa 
• Atom Count: 2507 
• Modelled Residue Count: 288 
• Deposited Residue Count: 310 
• Unique protein chains: 1

4QMX

MST3 in complex with SARACATINIB

• DOI: 10.2210/pdb4QMX/pdb

• Classification: Transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-06-16 Released: 2015-07-01 
• Deposition Author(s): Olesen, S.H., Watts, C., Zhu, J.-Y., Schonbrunn, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.218 
• R-Value Work: 0.179 

Literature

Discovery of Diverse Small-Molecule Inhibitors of Mammalian Sterile20-like Kinase 3 (MST3).

Olesen, S.H., Zhu, J.Y., Martin, M.P., Schonbrunn, E.

(2016) ChemMedChem 11: 1137-1144

• PubMed: 27135311 
• DOI: 10.1002/cmdc.201600115
• Primary Citation of Related Structures:  
  4QML, 4QMM, 4QMN, 4QMO, 4QMP, 4QMQ, 4QMS, 4QMT, 4QMU, 4QMV, 4QMW, 4QMX, 4QMY, 4QMZ, 4QNA, 4QO9


• PubMed Abstract: 
  

Increasing evidence suggests key roles for members of the mammalian Sterile20-like (MST) family of kinases in many aspects of biology. MST3 is a member of the STRIPAK complex, the deregulation of which has recently been associated with cancer cell migration and metastasis. Targeting MST3 with small-molecule inhibitors may be beneficial for the treatment of certain cancers, but little information exists on the potential of kinase inhibitor scaffolds to engage with MST3. In this study we screened MST3 against a library of 277 kinase inhibitors using differential scanning fluorimetry and confirmed 14 previously unknown MST3 inhibitors by X-ray crystallography. These compounds, of which eight are in clinical trials or FDA approved, comprise nine distinct chemical scaffolds that inhibit MST3 enzymatic activity with IC50 values between 0.003 and 23 μm. The structure-activity relationships explain the differential inhibitory activity of these compounds against MST3 and the structural basis for high binding potential, the information of which may serve as a framework for the rational design of MST3-selective inhibitors as potential therapeutics and to interrogate the function of this enzyme in diseased cells.

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Organizational Affiliation: 

Drug Discovery Department, Moffitt Cancer Center, Tampa, FL, 33612, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE 24	A	310	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H8H (Subject of Investigation/LOI)	B [auth A]	N-(5-CHLORO-1,3-BENZODIOXOL-4-YL)-7-[2-(4-METHYLPIPERAZIN-1-YL)ETHOXY]-5-(TETRAHYDRO-2H-PYRAN-4-YLOXY)QUINAZOLIN-4-AMINE C27 H32 Cl N5 O5 OUKYUETWWIPKQR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Binding Affinity Annotations
ID	Source	Binding Affinity
H8H	Binding MOAD:  4QMX	IC50: 1.10e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.218 
• R-Value Work: 0.179 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.551	α = 90
b = 55.119	β = 111.58
c = 60.64	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2014-06-16 
• Released Date: 2015-07-01 
Deposition Author(s): Olesen, S.H., Watts, C., Zhu, J.-Y., Schonbrunn, E.

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2016-06-15
  Changes: Database references
• Version 1.2: 2016-07-13
  Changes: Database references
• Version 1.3: 2018-04-11
  Changes: Data collection