6RSU

TBK1 in complex with Inhibitor compound 35


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.351 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.292 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of BAY-985, a Highly Selective TBK1/IKK epsilon Inhibitor.

Lefranc, J.Schulze, V.K.Hillig, R.C.Briem, H.Prinz, F.Mengel, A.Heinrich, T.Balint, J.Rengachari, S.Irlbacher, H.Stockigt, D.Bomer, U.Bader, B.Gradl, S.N.Nising, C.F.von Nussbaum, F.Mumberg, D.Panne, D.Wengner, A.M.

(2020) J Med Chem 63: 601-612

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01460
  • Primary Citation of Related Structures:  
    6RSR, 6RST, 6RSU

  • PubMed Abstract: 

    The serine/threonine kinase TBK1 (TANK-binding kinase 1) and its homologue IKKε are noncanonical members of the inhibitor of the nuclear factor κB (IκB) kinase family. These kinases play important roles in multiple cellular pathways and, in particular, in inflammation. Herein, we describe our investigations on a family of benzimidazoles and the identification of the potent and highly selective TBK1/IKKε inhibitor BAY-985. BAY-985 inhibits the cellular phosphorylation of interferon regulatory factor 3 and displays antiproliferative efficacy in the melanoma cell line SK-MEL-2 but showed only weak antitumor activity in the SK-MEL-2 human melanoma xenograft model.


  • Organizational Affiliation

    Pharmaceuticals, Research and Development , Bayer AG , 13353 Berlin , Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase TBK1663Homo sapiensMutation(s): 0 
Gene Names: TBK1NAK
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHD2 (Homo sapiens)
Explore Q9UHD2 
Go to UniProtKB:  Q9UHD2
PHAROS:  Q9UHD2
GTEx:  ENSG00000183735 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHD2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KJB (Subject of Investigation/LOI)
Query on KJB

Download Ideal Coordinates CCD File 
B [auth A]3,3,3-tris(fluoranyl)-1-[4-[(1~{R})-1-[2-[[(2~{S})-5-(5-propan-2-yloxypyrimidin-4-yl)-2,3-dihydro-1~{H}-benzimidazol-2-yl]amino]pyridin-4-yl]ethyl]piperazin-1-yl]propan-1-one
C28 H33 F3 N8 O2
PETZDHZEDSUUQC-CLYVBNDRSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.351 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.292 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.562α = 90
b = 136.562β = 90
c = 87.251γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description