6QAV

Crystal structure of ULK2 in complexed with MRT68921


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Conservation of structure, function and inhibitor binding in UNC-51-like kinase 1 and 2 (ULK1/2).

Chaikuad, A.Koschade, S.E.Stolz, A.Zivkovic, K.Pohl, C.Shaid, S.Ren, H.Lambert, L.J.Cosford, N.D.P.Brandts, C.H.Knapp, S.

(2019) Biochem.J. 476: 875-887

  • DOI: 10.1042/BCJ20190038
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Autophagy is essential for cellular homeostasis and when deregulated this survival mechanism has been associated with disease development. Inhibition of autophagy initiation by inhibiting the kinase ULK1 (Unc-51-like autophagy activating kinase 1) ha ...

    Autophagy is essential for cellular homeostasis and when deregulated this survival mechanism has been associated with disease development. Inhibition of autophagy initiation by inhibiting the kinase ULK1 (Unc-51-like autophagy activating kinase 1) has been proposed as a potential cancer therapy. While inhibitors and crystal structures of ULK1 have been reported, little is known about the other closely related kinase ULK2 (Unc-51-like autophagy activating kinase 2). Here, we present the crystal structure of ULK2 in complex with ATP competitive inhibitors. Surprisingly, the ULK2 structure revealed a dimeric assembly reminiscent of dimeric arrangements of auto-activating kinases suggesting a role for this association in ULK activation. Screening of a kinase focused library of pre-clinical and clinical compounds revealed several potent ULK1/2 inhibitors and good correlation of inhibitor-binding behavior with both ULK kinases. Aurora A was identified as a major off-target of currently used ULK1 inhibitors. Autophagic flux assays demonstrated that this off-target activity by strongly inducing autophagy in different cellular systems conferred an additional layer of complexity in the interpretation of cellular data. The data presented here provide structural models and chemical starting points for the development of ULK1/2 dual inhibitors with improved selectivity for future exploitation of autophagy inhibition.


    Organizational Affiliation

    German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,University Cancer Center Frankfurt (UCT), Goethe University, Frankfurt, Germany.,Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany knapp@pharmchem.uni-frankfurt.de chaikuad@pharmchem.uni-frankfurt.de.,Structural Genomics Consortium, BMLS, Goethe-University Frankfurt, 60438 Frankfurt, Germany.,Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany.,Institute of Biochemistry II, Goethe University School of Medicine, 60590 Frankfurt, Germany.,NCI Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, U.S.A.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase ULK2
A, B, C, D
280Homo sapiensMutation(s): 0 
Gene Names: ULK2 (KIAA0623)
EC: 2.7.11.1
Find proteins for Q8IYT8 (Homo sapiens)
Go to Gene View: ULK2
Go to UniProtKB:  Q8IYT8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HVH
Query on HVH

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Download CCD File 
A, B, C, D
~{N}-[3-[[5-cyclopropyl-2-[(2-methyl-3,4-dihydro-1~{H}-isoquinolin-6-yl)amino]pyrimidin-4-yl]amino]propyl]cyclobutanecarboxamide
C25 H34 N6 O
KKISLZKMBSCLSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.648α = 90.00
b = 69.050β = 97.93
c = 107.710γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
iMOSFLMdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-03-20
    Type: Data collection, Database references