7QUF

The STK17A (DRAK1) Kinase Domain Bound to CK156


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Illuminating the Dark: Highly Selective Inhibition of Serine/Threonine Kinase 17A with Pyrazolo[1,5- a ]pyrimidine-Based Macrocycles.

Kurz, C.G.Preuss, F.Tjaden, A.Cusack, M.Amrhein, J.A.Chatterjee, D.Mathea, S.Berger, L.M.Berger, B.T.Kramer, A.Weller, M.Weiss, T.Muller, S.Knapp, S.Hanke, T.

(2022) J Med Chem 65: 7799-7817

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00173
  • Primary Citation of Related Structures:  
    7QUE, 7QUF

  • PubMed Abstract: 

    Serine/threonine kinase 17A (death-associated protein kinase-related apoptosis-inducing protein kinase 1─DRAK1) is a part of the death-associated protein kinase (DAPK) family and belongs to the so-called dark kinome. Thus, the current state of knowledge of the cellular function of DRAK1 and its involvement in pathophysiological processes is very limited. Recently, DRAK1 has been implicated in tumorigenesis of glioblastoma multiforme (GBM) and other cancers, but no selective inhibitors of DRAK1 are available yet. To this end, we optimized a pyrazolo[1,5- a ]pyrimidine-based macrocyclic scaffold. Structure-guided optimization of this macrocyclic scaffold led to the development of CK156 ( 34 ), which displayed high in vitro potency ( K D = 21 nM) and selectivity in kinomewide screens. Crystal structures demonstrated that CK156 ( 34 ) acts as a type I inhibitor. However, contrary to studies using genetic knockdown of DRAK1, we have seen the inhibition of cell growth of glioma cells in 2D and 3D culture only at low micromolar concentrations.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase 17A
A, B
275Homo sapiensMutation(s): 0 
Gene Names: STK17ADRAK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UEE5 (Homo sapiens)
Explore Q9UEE5 
Go to UniProtKB:  Q9UEE5
PHAROS:  Q9UEE5
GTEx:  ENSG00000164543 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UEE5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F8I (Subject of Investigation/LOI)
Query on F8I

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
~{N}-~{tert}-butyl-7,10-dioxa-13,17,18,21-tetrazatetracyclo[12.5.2.1^{2,6}.0^{17,20}]docosa-1(20),2(22),3,5,14(21),15,18-heptaene-5-carboxamide
C21 H25 N5 O3
YCFFONJEHNSECY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.07α = 90
b = 83.066β = 90
c = 115.836γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description