Crystal structure of human TAK1/TAB1 fusion protein in complex with ligand 10

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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Discovery of a potent and highly selective transforming growth factor beta receptor-associated kinase 1 (TAK1) inhibitor by structure based drug design (SBDD)

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

(2016) Bioorg Med Chem 24: 4206-4217

  • DOI: https://doi.org/10.1016/j.bmc.2016.07.006
  • Primary Citation of Related Structures:  
    5JGA, 5JGB, 5JGD

  • PubMed Abstract: 

    A novel thienopyrimidinone analog was discovered as a potent and highly selective TAK1 inhibitor using the SBDD approach. TAK1 plays a key role in inflammatory and immune signaling, so TAK1 is considered to be an attractive molecular target for the treatment of human diseases (inflammatory disease, cancer, etc.). After the hit compound had been obtained, our modifications successfully increased TAK1 inhibitory activity and solubility, but metabolic stability was still unsatisfactory. To improve metabolic stability, we conducted metabolic identification. Although the obtained metabolite was fortunately a potent TAK1 inhibitor, its kinase selectivity was low. Subsequently, to achieve high kinase selectivity, we used SBDD to follow two strategies: one targeting unique amino acid residues in TAK1, especially the combination of Ser111 and Asn114; the other decreasing the interaction with Tyr106 at the hinge position in TAK1. As expected, our designed compound showed an excellent kinase selectivity profile in both an in-house and a commercially available panel assay of over 420 kinases and also retained its potent TAK1 inhibitory activity (TAK1 IC50=11nM).

  • Organizational Affiliation

    Research Division, Chugai Pharmaceutical Co,. Ltd, 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan. Electronic address: muraokatrs@chugai-pharm.co.jp.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TAK1 kinase - TAB1 chimera fusion protein315Homo sapiensMutation(s): 0 
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsO43318Q15750
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 6JV

Download Ideal Coordinates CCD File 
B [auth A]N-(2-methoxy-4-{[3-(4-methylpiperazin-1-yl)propyl]carbamoyl}phenyl)-4-oxo-3,4-dihydrothieno[3,2-d]pyrimidine-7-carboxamide
C23 H28 N6 O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
6JV BindingDB:  5JGB IC50: 13 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.711α = 90
b = 134.97β = 90
c = 143.169γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

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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: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description