Pyridopyrimidinone Derivatives as Potent and Selective c-Jun N-Terminal Kinase (JNK) inhibitors

Experimental Data Snapshot

  • Resolution: 2.06 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 

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Ligand Structure Quality Assessment 

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Pyridopyrimidinone Derivatives as Potent and Selective c-Jun N-Terminal Kinase (JNK) Inhibitors.

Zheng, K.Park, C.M.Iqbal, S.Hernandez, P.Park, H.LoGrasso, P.V.Feng, Y.

(2015) ACS Med Chem Lett 6: 413-418

  • DOI: https://doi.org/10.1021/ml500474d
  • Primary Citation of Related Structures:  
    4Y46, 4Y5H

  • PubMed Abstract: 

    A novel series of 2-aminopyridopyrimidinone based JNK (c-jun N-terminal kinase) inhibitors were discovered and developed. Structure-activity relationships (SARs) were systematically developed utilizing biochemical and cell based assays and in vitro and in vivo drug metabolism and pharmacokinetic (DMPK) studies. Through the optimization of lead compound 1, several potent and selective JNK inhibitors with high oral bioavailability were developed. Inhibitor 13 was a potent JNK3 inhibitor (IC50 = 15 nM), had high selectivity against p38 (IC50 > 10 μM), had high potency in functional cell based assays, and had high stability in human liver microsome (t 1/2 = 76 min), a clean CYP-450 inhibition profile, and excellent oral bioavailability (%F = 87). Moreover, cocrystal structures of compounds 13 and 22 in JNK3 were solved at 2.0 Å. These structures elucidated the binding mode (Type-I binding) and can pave the way for further inhibitor design of this pyridopyrimidinone scaffold for JNK inhibition.

  • Organizational Affiliation

    Medicinal Chemistry, Discovery Biology, Crystallography/Modeling Core Facility, Translational Research Institute, and Department of Molecular Therapeutics, The Scripps Research Institute , 130 Scripps Way, #2A1, Jupiter, Florida 33458, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 10366Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens)
Explore P53779 
Go to UniProtKB:  P53779
GTEx:  ENSG00000109339 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53779
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 519

Download Ideal Coordinates CCD File 
B [auth A]1-(trans-4-{[7-oxo-8-(propan-2-yl)-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl]amino}cyclohexyl)-3-propan-2-ylurea
C20 H30 N6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
519 BindingDB:  4Y5H IC50: min: 15, max: 66 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.06 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.708α = 90
b = 71.813β = 90
c = 107.802γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2015-05-06 
  • Deposition Author(s): Park, H.

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy