5GJF

Crystal structure of human TAK1/TAB1 fusion protein in complex with ligand 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Development of a Method for Converting a TAK1 Type I Inhibitor into a Type II or c-Helix-Out Inhibitor by Structure-Based Drug Design (SBDD)

Muraoka, T.Ide, M.Irie, M.Morikami, K.Miura, T.Nishihara, M.Kashiwagi, H.

(2016) Chem Pharm Bull (Tokyo) 64: 1622-1629

  • DOI: 10.1248/cpb.c16-00606
  • Primary Citation of Related Structures:  
    5GJD, 5GJG, 5GJF

  • PubMed Abstract: 
  • We have developed a method for converting a transforming growth factor-β-activated kinase 1 (TAK1) type I inhibitor into a type II or c-helix-out inhibitor by structure-based drug design (SBDD) to achieve an effective strategy for developing these different types of kinase inhibitor in parallel ...

    We have developed a method for converting a transforming growth factor-β-activated kinase 1 (TAK1) type I inhibitor into a type II or c-helix-out inhibitor by structure-based drug design (SBDD) to achieve an effective strategy for developing these different types of kinase inhibitor in parallel. TAK1 plays a key role in inflammatory and immune signaling, and is therefore considered to be an attractive molecular target for the treatment of human diseases (inflammatory disease, cancer, etc.). We have already reported novel type I TAK1 inhibitor, so we utilized its X-ray information to design a new chemical class type II and c-helix-out inhibitors. To develop the type II inhibitor, we superimposed the X-ray structure of our reported type I inhibitor onto a type II compound that inhibits multiple kinases, and used SBDD to design a new type II inhibitor. For the TAK1 c-helix-out inhibitor, we utilized the X-ray structure of a b-Raf c-helix-out inhibitor to design compounds, because TAK1 is located close to b-Raf in the Sugen kinase tree, so we considered that TAK1 would, similarly to b-Raf, form a c-helix-out conformation. The X-ray crystal structure of the inhibitors in complex with TAK1 confirmed the binding modes of the compounds we designed. This report is notable for being the first discovery of a c-helix-out inhibitor against TAK1.


    Organizational Affiliation

    Research Division, Chugai Pharmaceutical Co., Ltd.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TAK1 kinase - TAB1 chimera fusion proteinA315Homo sapiensMutation(s): 0 
Gene Names: MAP3K7TAK1
EC: 2.7.11.25
Find proteins for Q15750 (Homo sapiens)
Explore Q15750 
Go to UniProtKB:  Q15750
NIH Common Fund Data Resources
PHAROS  Q15750
Find proteins for O43318 (Homo sapiens)
Explore O43318 
Go to UniProtKB:  O43318
NIH Common Fund Data Resources
PHAROS  O43318
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6V4
Query on 6V4

Download Ideal Coordinates CCD File 
A
N-(2-isopropoxy-4-(4-methylpiperazine-1-carbonyl)phenyl)-2-(3-(3-phenylureido)phenyl)thiazole-4-carboxamide
C32 H34 N6 O4 S
YHONMSVJCMGHMF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.07α = 90
b = 132.96β = 90
c = 141.46γ = 90
Software Package:
Software NamePurpose
XDSdata processing
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection, Database references, Derived calculations