6HMP

Crystal structure of human Casein Kinase I delta in complex with a photoswitchable 2-Azoimidazole-based Inhibitor (compound 3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

2-Azo-, 2-diazocine-thiazols and 2-azo-imidazoles as photoswitchable kinase inhibitors: limitations and pitfalls of the photoswitchable inhibitor approach.

Schehr, M.Ianes, C.Weisner, J.Heintze, L.Muller, M.P.Pichlo, C.Charl, J.Brunstein, E.Ewert, J.Lehr, M.Baumann, U.Rauh, D.Knippschild, U.Peifer, C.Herges, R.

(2019) Photochem Photobiol Sci 18: 1398-1407

  • DOI: 10.1039/c9pp00010k
  • Primary Citation of Related Structures:  
    6HMP, 6HMR, 6HWV, 6HWU, 6HWT

  • PubMed Abstract: 
  • In photopharmacology, photoswitchable compounds including azobenzene or other diarylazo moieties exhibit bioactivity against a target protein typically in the slender E-configuration, whereas the rather bulky Z-configuration usually is pharmacologically less potent ...

    In photopharmacology, photoswitchable compounds including azobenzene or other diarylazo moieties exhibit bioactivity against a target protein typically in the slender E-configuration, whereas the rather bulky Z-configuration usually is pharmacologically less potent. Herein we report the design, synthesis and photochemical/inhibitory characterization of new photoswitchable kinase inhibitors targeting p38α MAPK and CK1δ. A well characterized inhibitor scaffold was used to attach arylazo- and diazocine moieties. When the isolated isomers, or the photostationary state (PSS) of isomers, were tested in commonly used in vitro kinase assays, however, only small differences in activity were observed. X-ray analyses of ligand-bound p38α MAPK and CK1δ complexes revealed dynamic conformational adaptations of the protein with respect to both isomers. More importantly, irreversible reduction of the azo group to the corresponding hydrazine was observed. Independent experiments revealed that reducing agents such as DTT (dithiothreitol) and GSH (glutathione) that are typically used for protein stabilization in biological assays were responsible. Two further sources of error are the concentration dependence of the E-Z-switching efficiency and artefacts due to incomplete exclusion of light during testing. Our findings may also apply to a number of previously investigated azobenzene-based photoswitchable inhibitors.


    Organizational Affiliation

    Otto Diels-Institute of Organic Chemistry, Christian Albrechts University Kiel, Otto-Hahn-Platz 4, 24118 Kiel, Germany. rherges@oc.uni-kiel.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Casein kinase I isoform deltaA, B314Homo sapiensMutation(s): 0 
Gene Names: CSNK1DHCKID
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.26 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P48730 (Homo sapiens)
Explore P48730 
Go to UniProtKB:  P48730
PHAROS:  P48730
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GEW (Subject of Investigation/LOI)
Query on GEW

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]3-(2,5-dimethoxyphenyl)-~{N}-[4-[5-(4-fluorophenyl)-2-[(~{E})-(4-fluorophenyl)diazenyl]-3-methyl-imidazol-4-yl]pyridin-2-yl]propanamide
C32 H28 F2 N6 O3
BBDJOFZXYVEURD-YMZYAJTMSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GEW Binding MOAD:  6HMP IC50: 218 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.819α = 90
b = 72.223β = 103.21
c = 89.161γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release