8ZML | pdb_00008zml

Structure of TNIK with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 
    0.326 (Depositor), 0.323 (DCC) 
  • R-Value Work: 
    0.256 (Depositor), 0.257 (DCC) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Discovery of Bis-imidazolecarboxamide Derivatives as Novel, Potent, and Selective TNIK Inhibitors for the Treatment of Idiopathic Pulmonary Fibrosis.

Aladinskiy, V.Kruse, C.Qin, L.Babin, E.Fan, Y.Andreev, G.Zhao, H.Fu, Y.Zhang, M.Ivanenkov, Y.Aliper, A.Zhavoronkov, A.Ren, F.

(2024) J Med Chem 67: 19121-19142

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01580
  • Primary Citation of Related Structures:  
    8ZML

  • PubMed Abstract: 

    Traf2- and Nck-interacting kinase (TNIK) has been identified as a promising therapeutic target for the treatment of fibrosis-driven diseases. Utilizing a structure-based drug design workflow, we developed a series of potent TNIK inhibitors that modulate the conformation of the gatekeeper Met105 side chain and access the TNIK back pocket. The lead optimization efforts culminated in the discovery of the recently reported compound 4 (INS018_055), a novel TNIK inhibitor. This molecule demonstrated excellent activity in both enzymatic and cell-based assays, along with high selectivity in a kinome panel. Further, in vitro and in vivo preclinical studies revealed favorable in vitro and in vivo DMPK properties. Results from multiple cell-based and animal models proved that compound 4 exhibits considerable antifibrotic and anti-inflammatory efficacy. Currently, phase II clinical trials of compound 4 are underway for the treatment of idiopathic pulmonary fibrosis (IPF).


  • Organizational Affiliation
    • Insilico Medicine AI Ltd., Level 6, Unit 08, Block A, IRENA HQ Building Masdar City, Abu Dhabi 145748, United Arab Emirates.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRAF2 and NCK-interacting protein kinase
A, B
303Homo sapiensMutation(s): 0 
Gene Names: TNIKKIAA0551
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKE5 (Homo sapiens)
Explore Q9UKE5 
Go to UniProtKB:  Q9UKE5
PHAROS:  Q9UKE5
GTEx:  ENSG00000154310 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKE5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free:  0.326 (Depositor), 0.323 (DCC) 
  • R-Value Work:  0.256 (Depositor), 0.257 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.889α = 90
b = 89.595β = 90
c = 97.577γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-05-28 
  • Deposition Author(s): Fan, Y.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Derived calculations, Structure summary
  • Version 1.2: 2025-12-10
    Changes: Database references