7O7J

Crystal structure of the human HIPK3 kinase domain bound to abemaciclib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Abemaciclib is a potent inhibitor of DYRK1A and HIP kinases involved in transcriptional regulation.

Kaltheuner, I.H.Anand, K.Moecking, J.Duster, R.Wang, J.Gray, N.S.Geyer, M.

(2021) Nat Commun 12: 6607-6607

  • DOI: 10.1038/s41467-021-26935-z
  • Primary Citation of Related Structures:  
    7O7I, 7O7J, 7O7K

  • PubMed Abstract: 
  • Homeodomain-interacting protein kinases (HIPKs) belong to the CMGC kinase family and are closely related to dual-specificity tyrosine phosphorylation-regulated kinases (DYRKs). HIPKs are regulators of various signaling pathways and involved in the pathology of cancer, chronic fibrosis, diabetes, and multiple neurodegenerative diseases ...

    Homeodomain-interacting protein kinases (HIPKs) belong to the CMGC kinase family and are closely related to dual-specificity tyrosine phosphorylation-regulated kinases (DYRKs). HIPKs are regulators of various signaling pathways and involved in the pathology of cancer, chronic fibrosis, diabetes, and multiple neurodegenerative diseases. Here, we report the crystal structure of HIPK3 in its apo form at 2.5 Å resolution. Recombinant HIPKs and DYRK1A are auto-activated and phosphorylate the negative elongation factor SPT5, the transcription factor c-Myc, and the C-terminal domain of RNA polymerase II, suggesting a direct function in transcriptional regulation. Based on a database search, we identified abemaciclib, an FDA-approved Cdk4/Cdk6 inhibitor used for the treatment of metastatic breast cancer, as potent inhibitor of HIPK2, HIPK3, and DYRK1A. We determined the crystal structures of HIPK3 and DYRK1A bound to abemaciclib, showing a similar binding mode to the hinge region of the kinase as observed for Cdk6. Remarkably, DYRK1A is inhibited by abemaciclib to the same extent as Cdk4/Cdk6 in vitro, raising the question of whether targeting of DYRK1A contributes to the transcriptional inhibition and therapeutic activity of abemaciclib.


    Organizational Affiliation

    Institute of Structural Biology, University of Bonn, Bonn, Germany. matthias.geyer@uni-bonn.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Homeodomain-interacting protein kinase 3A404Homo sapiensMutation(s): 0 
Gene Names: HIPK3DYRK6FIST3PKY
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H422 (Homo sapiens)
Explore Q9H422 
Go to UniProtKB:  Q9H422
PHAROS:  Q9H422
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6ZV (Subject of Investigation/LOI)
Query on 6ZV

Download Ideal Coordinates CCD File 
B [auth A]N-{5-[(4-ethylpiperazin-1-yl)methyl]pyridin-2-yl}-5-fluoro-4-[4-fluoro-2-methyl-1-(propan-2-yl)-1H-benzimidazol-6-yl]py rimidin-2-amine
C27 H32 F2 N8
UZWDCWONPYILKI-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
AL-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.064α = 90
b = 81.064β = 90
c = 178.82γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyGE 976/9-2

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references