1EH4

BINARY COMPLEX OF CASEIN KINASE-1 FROM S. POMBE WITH AN ATP COMPETITIVE INHIBITOR, IC261


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.304 (Depositor) 
  • R-Value Work: 
    0.224 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted IC1Click on this verticalbar to view details

This is version 1.5 of the entry. See complete history


Literature

Crystal Structure of a Conformation-Selective Casein Kinase-1 Inhibitor

Mashhoon, N.Demaggio, A.J.Tereshko, V.Bergmeier, S.C.Egli, M.Hoekstra, M.F.Kuret, J.

(2000) J Biol Chem 275: 20052-20060

  • DOI: https://doi.org/10.1074/jbc.M001713200
  • Primary Citation of Related Structures:  
    1EH4

  • PubMed Abstract: 

    Members of the casein kinase-1 family of protein kinases play an essential role in cell regulation and disease pathogenesis. Unlike most protein kinases, they appear to function as constitutively active enzymes. As a result, selective pharmacological inhibitors can play an important role in dissection of casein kinase-1-dependent processes. To address this need, new small molecule inhibitors of casein kinase-1 acting through ATP-competitive and ATP-noncompetitive mechanisms were isolated on the basis of in vitro screening. Here we report the crystal structure of 3-[(2,4,6-trimethoxyphenyl) methylidenyl]-indolin-2-one (IC261), an ATP-competitive inhibitor with differential activity among casein kinase-1 isoforms, in complex with the catalytic domain of fission yeast casein kinase-1 refined to a crystallographic R-factor of 22.4% at 2.8 A resolution. The structure reveals that IC261 stabilizes casein kinase-1 in a conformation midway between nucleotide substrate liganded and nonliganded conformations. We propose that adoption of this conformation by casein kinase-1 family members stabilizes a delocalized network of side chain interactions and results in a decreased dissociation rate of inhibitor.


  • Organizational Affiliation

    Center for Biotechnology, Ohio State University College of Medicine, Columbus, Ohio 43210, ICOS Corporation, Bothell, Washington 98021, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CASEIN KINASE-1
A, B
298Schizosaccharomyces pombeMutation(s): 0 
EC: 2.7.1 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt
Find proteins for P40233 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P40233 
Go to UniProtKB:  P40233
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40233
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IC1
Query on IC1

Download Ideal Coordinates CCD File 
I [auth A],
O [auth B]
3-[(2,4,6-TRIMETHOXY-PHENYL)-METHYLENE]-INDOLIN-2-ONE
C18 H17 N O4
JBJYTZXCZDNOJW-JLHYYAGUSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.304 (Depositor) 
  • R-Value Work:  0.224 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.5α = 90
b = 113.5β = 90
c = 110.4γ = 120
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
bioteXdata reduction
bioteXdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted IC1Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-09-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2024-03-13
    Changes: Source and taxonomy, Structure summary