5MQV

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.154 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 10.3390/molecules22040522
  • Primary Citation of Related Structures:  

  • 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 ef ...

    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 (IC50 CK1δ = 4 nM, IC50 CK1ε = 25 nM), 12a (IC50 CK1δ = 19 nM, IC50 CK1ε = 227 nM), and 16b (IC50 CK1δ = 8 nM, IC50 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 (EC50 = 3.5 µM) and Panc89 (EC50 = 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase I isoform delta
A, B, C, D, E, F
314Homo sapiensMutation(s): 0 
Gene Names: CSNK1D (HCKID)
EC: 2.7.11.1
Find proteins for P48730 (Homo sapiens)
Go to Gene View: CSNK1D
Go to UniProtKB:  P48730
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
D5Q
Query on D5Q

Download SDF File 
Download CCD File 
A, B, C, D, E, F
4-(2,5-Dimethoxyphenyl)-N-(4-(5-(4-fluorphenyl)-2-(methylthio)-1H-imidazol-4-yl)-pyridin-2-yl)-1-methyl-1H-pyrrole-2-carboxamide
C29 H26 F N5 O3 S
SQTWIUXTIUIKOJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D5QIC50: 8 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.154 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 197.934α = 90.00
b = 127.276β = 113.63
c = 154.780γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release