8QLQ

Human MST3 (STK24) kinase in complex with macrocyclic inhibitor JA310


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Synthesis of Pyrazole-Based Macrocycles Leads to a Highly Selective Inhibitor for MST3.

Amrhein, J.A.Berger, L.M.Balourdas, D.I.Joerger, A.C.Menge, A.Kramer, A.Frischkorn, J.M.Berger, B.T.Elson, L.Kaiser, A.Schubert-Zsilavecz, M.Muller, S.Knapp, S.Hanke, T.

(2024) J Med Chem 67: 674-690

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01980
  • Primary Citation of Related Structures:  
    8QLQ

  • PubMed Abstract: 

    MST1, MST2, MST3, MST4, and YSK1 are conserved members of the mammalian sterile 20-like serine/threonine (MST) family that regulate cellular functions such as proliferation and migration. The MST3 isozyme plays a role in regulating cell growth and apoptosis, and its dysregulation has been linked to high-grade tumors. To date, there are no isoform-selective inhibitors that could be used for validating the role of MST3 in tumorigenesis. We designed a series of 3-aminopyrazole-based macrocycles based on the structure of a promiscuous inhibitor. By varying the moieties targeting the solvent-exposed region and optimizing the linker, macrocycle JA310 ( 21c ) was synthesized. JA310 exhibited high cellular potency for MST3 (EC 50 = 106 nM) and excellent kinome-wide selectivity. The crystal structure of the MST3-JA310 complex provided intriguing insights into the binding mode, which is associated with large-scale structural rearrangements. In summary, JA310 demonstrates the utility of macrocyclization for the design of highly selective inhibitors and presents the first chemical probe for MST3.


  • Organizational Affiliation

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


Macromolecules
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
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6E0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VY0 (Subject of Investigation/LOI)
Query on VY0

Download Ideal Coordinates CCD File 
B [auth A]macrocyclic inhibitor
C17 H19 N7 O
XBWKVZHZUZNMJE-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.127α = 90
b = 79.753β = 90
c = 100.537γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyJO 1473/1-3
The Structural Genomics Consortium (SGC)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-08
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references