6F26

Crystal structure of human Casein Kinase I delta in complex with compound 31b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Design, Synthesis and Biological Evaluation of Isoxazole-Based CK1 Inhibitors Modified with Chiral Pyrrolidine Scaffolds.

Luxenburger, A.Schmidt, D.Ianes, C.Pichlo, C.Kruger, M.von Drathen, T.Brunstein, E.Gainsford, G.J.Baumann, U.Knippschild, U.Peifer, C.

(2019) Molecules 24: --

  • DOI: 10.3390/molecules24050873
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In this study, we report on the modification of a 3,4-diaryl-isoxazole-based CK1 inhibitor with chiral pyrrolidine scaffolds to develop potent and selective CK1 inhibitors. The pharmacophore of the lead structure was extended towards the ribose pocke ...

    In this study, we report on the modification of a 3,4-diaryl-isoxazole-based CK1 inhibitor with chiral pyrrolidine scaffolds to develop potent and selective CK1 inhibitors. The pharmacophore of the lead structure was extended towards the ribose pocket of the adenosine triphosphate (ATP) binding site driven by structure-based drug design. For an upscale compatible multigram synthesis of the functionalized pyrrolidine scaffolds, we used a chiral pool synthetic route starting from methionine. Biological evaluation of key compounds in kinase and cellular assays revealed significant effects of the scaffolds towards activity and selectivity, however, the absolute configuration of the chiral moieties only exhibited a limited effect on inhibitory activity. X-ray crystallographic analysis of ligand-CK1δ complexes confirmed the expected binding mode of the 3,4-diaryl-isoxazole inhibitors. Surprisingly, the original compounds underwent spontaneous Pictet-Spengler cyclization with traces of formaldehyde during the co-crystallization process to form highly potent new ligands. Our data suggests chiral "ribose-like" pyrrolidine scaffolds have interesting potential for modifications of pharmacologically active compounds.


    Organizational Affiliation

    Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt 5040, New Zealand. Andreas.Luxenburger@vuw.ac.nz.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase I isoform delta
A, B
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
C9Z
Query on C9Z

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Download CCD File 
A, B
(9~{S},10~{S},11~{R})-~{N}-[4-[3-(4-fluorophenyl)-5-propan-2-yl-1,2-oxazol-4-yl]pyridin-2-yl]-4-(4-methoxyphenyl)-10,11-bis(oxidanyl)-1,7-diazatricyclo[7.3.0.0^{3,7}]dodeca-3,5-diene-6-carboxamide
C35 H34 F N5 O5
VRODZCFGQSWGFE-FBXLTAPESA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.075α = 90.00
b = 72.956β = 90.15
c = 90.015γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release