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 

wwPDB Validation 3D Report Full Report


This is version 1.0 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. 64: 1622-1629

  • DOI: 10.1248/cpb.c16-00606
  • Primary Citation of Related Structures:  

  • 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 di ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TAK1 kinase - TAB1 chimera fusion protein
A
315Homo sapiensMutation(s): 0 
Gene Names: TAB1 (MAP3K7IP1), MAP3K7 (TAK1)
EC: 2.7.11.25
Find proteins for Q15750 (Homo sapiens)
Go to Gene View: TAB1
Go to UniProtKB:  Q15750
Find proteins for O43318 (Homo sapiens)
Go to Gene View: MAP3K7
Go to UniProtKB:  O43318
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6V4
Query on 6V4
Download SDF File 
Download 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 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 58.070α = 90.00
b = 132.960β = 90.00
c = 141.460γ = 90.00
Software Package:
Software NamePurpose
XDSdata processing
REFMACrefinement
MOLREPphasing
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-16
    Type: Initial release