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.

Macromolecule Content

• Total Structure Weight: 36.50 kDa 
• Atom Count: 2575 
• Modelled Residue Count: 294 
• Deposited Residue Count: 315 
• Unique protein chains: 1

4GS6

Irreversible Inhibition of TAK1 Kinase by 5Z-7-Oxozeaenol

• PDB DOI: 10.2210/pdb4GS6/pdb

• Classification: Transferase/Transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-08-27 Released: 2013-01-23 
• Deposition Author(s): Larsen, N.A., Ferguson, A.D., Wu, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.245 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 

Literature

Mechanism and In Vitro Pharmacology of TAK1 Inhibition by (5Z)-7-Oxozeaenol.

Wu, J., Powell, F., Larsen, N.A., Lai, Z., Byth, K.F., Read, J., Gu, R.F., Roth, M., Toader, D., Saeh, J.C., Chen, H.

(2013) ACS Chem Biol 8: 643-650

• PubMed: 23272696 
• DOI: 10.1021/cb3005897
• Primary Citation of Related Structures:  
  4GS6


• PubMed Abstract: 
  

Transforming growth factor-β activated kinase-1 (TAK1) is a member of the mitogen-activated protein kinase kinase kinase (MAP3K) family that regulates several signaling pathways including NF-κB signal transduction and p38 activation. TAK1 deregulation has been implicated in human diseases including cancer and inflammation. Here, we show that, in addition to its kinase activity, TAK1 has intrinsic ATPase activity, that (5Z)-7-Oxozeaenol irreversibly inhibits TAK1, and that sensitivity to (5Z)-7-Oxozeaenol inhibition in hematological cancer cell lines is NRAS mutation status and TAK1 pathway dependent. X-ray crystallographic and mass spectrometric studies showed that (5Z)-7-Oxozeaenol forms a covalent complex with TAK1. Detailed biochemical characterization revealed that (5Z)-7-Oxozeaenol inhibited both the kinase and the ATPase activity of TAK1 following a bi-phase kinetics, consistent with the irreversible inhibition mechanism. In DoHH2 cells, (5Z)-7-Oxozeaenol potently inhibited the p38 phosphorylation driven by TAK1, and the inhibition lasted over 6 h after withdrawal of (5Z)-7-Oxozeaenol. Profiling (5Z)-7-Oxozeaenol in a panel of hematological cancer cells showed that sensitive cell lines tended to carry NRAS mutations and that genes in TAK1 regulated pathways were enriched in sensitive cell lines. Taken together, we have elucidated the molecular mechanism of a TAK1 irreversible inhibitor and laid the foundation for designing next generation TAK1 irreversible inhibitors. The NRAS-TAK1-Wnt signaling network discerned in our study may prove to be useful in patient selection for TAK1 targeted agents in hematological cancers.

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Organizational Affiliation: 

Discovery Sciences, AstraZeneca R&D Boston, Waltham, MA 02451, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tak1-Tab1 fusion protein	A	315	Homo sapiens	Mutation(s): 0  Gene Names: MAP3K7, TAK1, TAB1, MAP3K7IP1 EC: 2.7.11.25
UniProt & NIH Common Fund Data Resources
Find proteins for Q15750 (Homo sapiens) Explore Q15750  Go to UniProtKB:  Q15750
PHAROS:  Q15750 GTEx:  ENSG00000100324
Find proteins for O43318 (Homo sapiens) Explore O43318  Go to UniProtKB:  O43318
PHAROS:  O43318 GTEx:  ENSG00000135341
UniProt Groups	O43318Q15750

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1FM	L [auth A]	(3S,5Z,8S,9S,11E)-8,9,16-trihydroxy-14-methoxy-3-methyl-3,4,9,10-tetrahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione C19 H22 O7 NEQZWEXWOFPKOT-BYRRXHGESA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1FM	PDBBind:  4GS6	Ki: 71 (nM) from 1 assay(s)
	BindingDB:  4GS6	IC50: min: 5.6, max: 1300 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.245 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.138	α = 90
b = 133.867	β = 90
c = 142.129	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
BUSTER	refinement
d*TREK	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-08-27 
• Released Date: 2013-01-23 
Deposition Author(s): Larsen, N.A., Ferguson, A.D., Wu, J.

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2013-03-27
  Changes: Database references
• Version 1.2: 2017-08-02
  Changes: Refinement description, Source and taxonomy