7NTH

Structure of TAK1 in complex with compound 54


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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Literature

Discovery of 2,4-1 H -Imidazole Carboxamides as Potent and Selective TAK1 Inhibitors.

Veerman, J.J.N.Bruseker, Y.B.Damen, E.Heijne, E.H.van Bruggen, W.Hekking, K.F.W.Winkel, R.Hupp, C.D.Keefe, A.D.Liu, J.Thomson, H.A.Zhang, Y.Cuozzo, J.W.McRiner, A.J.Mulvihill, M.J.van Rijnsbergen, P.Zech, B.Renzetti, L.M.Babiss, L.Muller, G.

(2021) ACS Med Chem Lett 12: 555-562

  • DOI: 10.1021/acsmedchemlett.0c00547
  • Primary Citation of Related Structures:  
    7NTH, 7NTI

  • PubMed Abstract: 
  • Herein we report the discovery of 2,4-1 H -imidazole carboxamides as novel, biochemically potent, and kinome selective inhibitors of transforming growth factor β-activated kinase 1 (TAK1). The target was subjected to a DNA-encoded chemical library (DECL) screen ...

    Herein we report the discovery of 2,4-1 H -imidazole carboxamides as novel, biochemically potent, and kinome selective inhibitors of transforming growth factor β-activated kinase 1 (TAK1). The target was subjected to a DNA-encoded chemical library (DECL) screen. After hit analysis a cluster of compounds was identified, which was based on a central pyrrole-2,4-1 H -dicarboxamide scaffold, showing remarkable kinome selectivity. A scaffold-hop to the corresponding imidazole resulted in increased biochemical potency. Next, X-ray crystallography revealed a distinct binding mode compared to other TAK1 inhibitors. A benzylamide was found in a perpendicular orientation with respect to the core hinge-binding imidazole. Additionally, an unusual amide flip was observed in the kinase hinge region. Using structure-based drug design (SBDD), key substitutions at the pyrrolidine amide and the glycine resulted in a significant increase in biochemical potency.


    Organizational Affiliation

    AnavoTherapeutics BV, J.H. Oortweg 19, 2333 CH Leiden, The Netherlands.



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 1A315Homo sapiensMutation(s): 0 
Gene Names: MAP3K7TAK1TAB1MAP3K7IP1
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
URW
Query on URW

Download Ideal Coordinates CCD File 
F [auth A]2-[[5-[[2-[bis(fluoranyl)methoxy]phenyl]methyl-[(2~{R})-1-(methylamino)-1-oxidanylidene-propan-2-yl]carbamoyl]-1~{H}-imidazol-2-yl]carbonyl]isoindole-5-carboxamide
C26 H24 F2 N6 O5
QTSQRRSNHSLXPH-CQSZACIVSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.421α = 90
b = 134.783β = 90
c = 145.449γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references