5AX9

Crystal structure of the kinase domain of human TRAF2 and NCK-interacting protein kinase in complex with compund 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

TNIK inhibition abrogates colorectal cancer stemness

Masuda, M.Uno, Y.Ohbayashi, N.Ohata, H.Mimata, A.Kukimoto-Niino, M.Moriyama, H.Kashimoto, S.Inoue, T.Goto, N.Okamoto, K.Shirouzu, M.Sawa, M.Yamada, T.

(2016) Nat Commun 7: 12586-12586

  • DOI: 10.1038/ncomms12586
  • Primary Citation of Related Structures:  
    5AX9, 5D7A, 5CWZ

  • PubMed Abstract: 
  • Canonical Wnt/β-catenin signalling is essential for maintaining intestinal stem cells, and its constitutive activation has been implicated in colorectal carcinogenesis. We and others have previously identified Traf2- and Nck-interacting kinase (TNIK) as an essential regulatory component of the T-cell factor-4 and β-catenin transcriptional complex ...

    Canonical Wnt/β-catenin signalling is essential for maintaining intestinal stem cells, and its constitutive activation has been implicated in colorectal carcinogenesis. We and others have previously identified Traf2- and Nck-interacting kinase (TNIK) as an essential regulatory component of the T-cell factor-4 and β-catenin transcriptional complex. Consistent with this, Tnik-deficient mice are resistant to azoxymethane-induced colon tumorigenesis, and Tnik(-/-)/Apc(min/+) mutant mice develop significantly fewer intestinal tumours. Here we report the first orally available small-molecule TNIK inhibitor, NCB-0846, having anti-Wnt activity. X-ray co-crystal structure analysis reveals that NCB-0846 binds to TNIK in an inactive conformation, and this binding mode seems to be essential for Wnt inhibition. NCB-0846 suppresses Wnt-driven intestinal tumorigenesis in Apc(min/+) mice and the sphere- and tumour-forming activities of colorectal cancer cells. TNIK is required for the tumour-initiating function of colorectal cancer stem cells. Its inhibition is a promising therapeutic approach.


    Organizational Affiliation

    Division of Chemotherapy and Clinical Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRAF2 and NCK-interacting protein kinaseA, B, C308Homo sapiensMutation(s): 0 
Gene Names: TNIKKIAA0551
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKE5 (Homo sapiens)
Explore Q9UKE5 
Go to UniProtKB:  Q9UKE5
PHAROS:  Q9UKE5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4KT (Subject of Investigation/LOI)
Query on 4KT

Download Ideal Coordinates CCD File 
D [auth A], F [auth B], H [auth C]4-methoxy-3-[2-[(3-methoxy-4-morpholin-4-yl-phenyl)amino]pyridin-4-yl]benzenecarbonitrile
C24 H24 N4 O3
JKDVQSBZXOTCNO-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A], G [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
4KT BindingDB:  5AX9 IC50: min: 8, max: 6300 (nM) from 2 assay(s)
Binding MOAD:  5AX9 IC50: 8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.208 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.178α = 90
b = 123.204β = 90
c = 157.652γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-09-07
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection, Derived calculations