Crystal structure of human Casein Kinase I delta in complex with 4-(2,5-Dimethoxyphenyl)-N-(4-(5-(4-fluorphenyl)-2-(methylthio)-1H-imidazol-4-yl)-pyridin-2-yl)-1-methyl-1H-pyrrole-2-carboxamide

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

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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
Casein kinase I isoform delta
A, B, C, D, E
A, B, C, D, E, F
314Homo sapiensMutation(s): 0 
EC: (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P48730 (Homo sapiens)
Explore P48730 
Go to UniProtKB:  P48730
PHAROS:  P48730
GTEx:  ENSG00000141551 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48730
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on D5Q

Download Ideal Coordinates CCD File 
BA [auth E]
EA [auth F]
G [auth A]
K [auth B]
P [auth C]
BA [auth E],
EA [auth F],
G [auth A],
K [auth B],
P [auth C],
V [auth D]
C29 H26 F N5 O3 S
Query on PO4

Download Ideal Coordinates CCD File 
AA [auth D]
CA [auth E]
DA [auth E]
FA [auth F]
GA [auth F]
AA [auth D],
CA [auth E],
DA [auth E],
FA [auth F],
GA [auth F],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
O4 P
Binding Affinity Annotations 
IDSourceBinding Affinity
D5Q Binding MOAD:  5MQV IC50: 8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.934α = 90
b = 127.276β = 113.63
c = 154.78γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction

Structure Validation

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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: 2024-01-17
    Changes: Data collection, Database references, Refinement description