Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 106.67 kDa 
• Atom Count: 6921 
• Modelled Residue Count: 838 
• Deposited Residue Count: 924 
• Unique protein chains: 1

5AX9

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

• PDB DOI: 10.2210/pdb5AX9/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Baculovirus expression vector pFastBac1-HM
• Mutation(s): No 


• Deposited: 2015-07-21 Released: 2016-07-27 
• Deposition Author(s): Ohbayashi, N., Kukimoto-Niino, M., Yamada, T., Shirouzu, M.

---

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 

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

• PubMed: 27562646 
• DOI: 10.1038/ncomms12586
• Primary Citation of Related Structures:  
  5AX9, 5CWZ, 5D7A


• 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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRAF2 and NCK-interacting protein kinase	A, B, C	308	Homo sapiens	Mutation(s): 0  Gene Names: TNIK, KIAA0551 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 GTEx:  ENSG00000154310

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4KT	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
SO4	E [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding 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 = 47.178	α = 90
b = 123.204	β = 90
c = 157.652	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-07-21 
• Released Date: 2016-07-27 
Deposition Author(s): Ohbayashi, N., Kukimoto-Niino, M., Yamada, T., Shirouzu, M.

Revision History  

• 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