Human p38alpha MAPK in complex with imidazolyl pyridine inhibitor 11b

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Optimized 4,5-Diarylimidazoles as Potent/Selective Inhibitors of Protein Kinase CK1 delta and Their Structural Relation to p38 alpha MAPK.

Halekotte, J.Witt, L.Ianes, C.Kruger, M.Buhrmann, M.Rauh, D.Pichlo, C.Brunstein, E.Luxenburger, A.Baumann, U.Knippschild, U.Bischof, J.Peifer, C.

(2017) Molecules 22

  • DOI: https://doi.org/10.3390/molecules22040522
  • Primary Citation of Related Structures:  
    5ML5, 5MQV

  • PubMed Abstract: 

    The involvement of protein kinase CK1δ in the pathogenesis of severe disorders such as Alzheimer's disease, amyotrophic lateral sclerosis, familial advanced sleep phase syndrome, and cancer has dramatically increased interest in the development of effective small molecule inhibitors for both therapeutic application and basic research. Unfortunately, the design of CK1 isoform-specific compounds has proved to be highly complicated due to the existence of six evolutionarily conserved human CK1 members that possess similar, different, or even opposite physiological and pathophysiological implications. Consequently, only few potent and selective CK1δ inhibitors have been reported so far and structurally divergent approaches are urgently needed in order to establish SAR that might enable complete discrimination of CK1 isoforms and related p38α MAPK. In this study we report on design and characterization of optimized 4,5-diarylimidazoles as highly effective ATP-competitive inhibitors of CK1δ with compounds 11b (IC 50 CK1δ = 4 nM, IC 50 CK1ε = 25 nM), 12a (IC 50 CK1δ = 19 nM, IC 50 CK1ε = 227 nM), and 16b (IC 50 CK1δ = 8 nM, IC 50 CK1ε = 81 nM) being among the most potent CK1δ-targeting agents published to date. Inhibitor compound 11b , displaying potential as a pharmacological tool, has further been profiled over a panel of 321 protein kinases exhibiting high selectivity. Cellular efficacy has been evaluated in human pancreatic cancer cell lines Colo357 (EC 50 = 3.5 µM) and Panc89 (EC 50 = 1.5 µM). SAR is substantiated by X-ray crystallographic analysis of 16b in CK1δ and 11b in p38α.

  • Organizational Affiliation

    Institute of Pharmacy, Christian-Albrechts-University of Kiel, Gutenbergstraße 76, D-24118 Kiel, Germany. jhalekotte@pharmazie.uni-kiel.de.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14360Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
GTEx:  ENSG00000112062 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16539
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1VI

Download Ideal Coordinates CCD File 
E [auth A]3-(2,5-dimethoxyphenyl)-~{N}-[4-[4-(4-fluorophenyl)-2-methylsulfanyl-1~{H}-imidazol-5-yl]pyridin-2-yl]propanamide
C26 H25 F N4 O3 S
Query on BOG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
octyl beta-D-glucopyranoside
C14 H28 O6
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.5α = 90
b = 69.39β = 90
c = 74.14γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Structure summary