7S1N

N-Aromatic-Substituted Indazole Derivatives as Brain Penetrant and Orally Bioavailable JNK3 Inhibitors

  • Classification: TRANSFERASE/Inhibitor
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2021-09-02 Released: 2021-11-03 
  • Deposition Author(s): Park, H.
  • Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

N -Aromatic-Substituted Indazole Derivatives as Brain-Penetrant and Orally Bioavailable JNK3 Inhibitors.

Feng, Y.Park, H.Ryu, J.C.Yoon, S.O.

(2021) ACS Med Chem Lett 12: 1546-1552

  • DOI: https://doi.org/10.1021/acsmedchemlett.1c00334
  • Primary Citation of Related Structures:  
    7S1N

  • PubMed Abstract: 

    An indazole/aza-indazole scaffold was developed as a novel chemotype for JNK3 inhibition. Extensive structure activity relationship (SAR) studies utilizing various in vitro and in vivo assays led to potent and highly selective JNK3 inhibitors with good oral bioavailability and high brain penetration. One lead compound, 29 , was a potent and selective JNK3 inhibitor (IC 50 = 0.005 μM) that had significant inhibition (>80% at 1 μM) to only JNK3 and JNK2 in a panel profiling of 374 wild-type kinases, had high potency in functional cell-based assays, had high stability in the human liver microsome ( t 1/2 = 92 min), and was orally bioavailable and brain penetrant (brain/plasma ratio: 56%). The cocrystal structure of 29 in human JNK3 at a 2.1 Å resolution showed that indazole or aza-indazole-based JNK3 inhibitors demonstrated a type I kinase inhibition/binding.


  • Organizational Affiliation

    Reaction Biology Corporation, One Great Valley Parkway, Malvern, Pennsylvania 19355, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 10464Homo sapiensMutation(s): 0 
Gene Names: MAPK10JNK3JNK3APRKM10SAPK1B
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens)
Explore P53779 
Go to UniProtKB:  P53779
PHAROS:  P53779
GTEx:  ENSG00000109339 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53779
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
86C (Subject of Investigation/LOI)
Query on 86C

Download Ideal Coordinates CCD File 
B [auth A]4-[5-(2-chloro-6-fluoroanilino)-6-methyl-1H-pyrazolo[3,4-b]pyridin-1-yl]-N-(oxetan-3-yl)thiophene-2-carboxamide
C21 H17 Cl F N5 O2 S
KDMADGZAPDHVHE-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
86C BindingDB:  7S1N IC50: min: 5, max: 387 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.271α = 90
b = 71.138β = 90
c = 107.798γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2021-11-03 
  • Deposition Author(s): Park, H.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesRO1AG055059

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description