5JH6

Crystal structure of TL10-92 bound to TAK1-TAB1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

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Literature

Structure-guided development of covalent TAK1 inhibitors.

Tan, L., Gurbani, D., Weisberg, E.L., Hunter, J.C., Li, L., Jones, D.S., Ficarro, S.B., Mowafy, S., Tam, C.P., Rao, S., Du, G., Griffin, J.D., Sorger, P.K., Marto, J.A., Westover, K.D., Gray, N.S.

(2017) Bioorg Med Chem 25: 838-846

  • DOI: https://doi.org/10.1016/j.bmc.2016.11.035
  • Primary Citation of Related Structures:  
    5E7R, 5J7S, 5J8I, 5J9L, 5JH6, 5JK3

  • PubMed Abstract: 

    • TAK1 (transforming growth factor-β-activated kinase 1) is an essential intracellular mediator of cytokine and growth factor signaling and a potential therapeutic target for the treatment of immune diseases and cancer. Herein we report development of a series of 2,4-disubstituted pyrimidine covalent TAK1 inhibitors that target Cys174, a residue immediately adjacent to the 'DFG-motif' of the kinase activation loop ...

    TAK1 (transforming growth factor-β-activated kinase 1) is an essential intracellular mediator of cytokine and growth factor signaling and a potential therapeutic target for the treatment of immune diseases and cancer. Herein we report development of a series of 2,4-disubstituted pyrimidine covalent TAK1 inhibitors that target Cys174, a residue immediately adjacent to the 'DFG-motif' of the kinase activation loop. Co-crystal structures of TAK1 with candidate compounds enabled iterative rounds of structure-based design and biological testing to arrive at optimized compounds. Lead compounds such as 2 and 10 showed greater than 10-fold biochemical selectivity for TAK1 over the closely related kinases MEK1 and ERK1 which possess an equivalently positioned cysteine residue. These compounds are smaller, more easily synthesized, and exhibit a different spectrum of kinase selectivity relative to previously reported macrocyclic natural product TAK1 inhibitors such as 5Z-7-oxozeanol.

    Organizational Affiliation: 

    Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA. Electronic address: Nathanael_Gray@dfci.harvard.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase 7,TGF-beta-activated kinase 1 and MAP3K7-binding protein 1314Homo sapiensMutation(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
Find proteins for O43318 (Homo sapiens)
Explore O43318 
Go to UniProtKB:  O43318
PHAROS:  O43318
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsO43318Q15750
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T92
Query on T92
Download Ideal Coordinates CCD File 
B [auth A]2-[(5-chloro-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]phenyl prop-2-enoate
C24 H25 Cl N6 O2
YEUSGXFRXSLYPA-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
UD1 BindingDB:  5JH6 IC50: 3.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.303α = 90
b = 133.579β = 90
c = 145.697γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesCPRIT R1207 and CPRIT RP140233

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description