3UZP

crystal structure of ck1d with PF670462 from P21 crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.222 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the interaction between casein kinase 1 delta and a potent and selective inhibitor.

Long, A.Zhao, H.Huang, X.

(2012) J Med Chem 55: 956-960

  • DOI: 10.1021/jm201387s
  • Primary Citation of Related Structures:  
    3UYS, 3UYT, 3UZP

  • PubMed Abstract: 
  • Casein kinase 1 delta (CK1δ) and its closest homologue CK1ε are key regulators of diverse cellular growth and survival processes such as Wnt signaling, DNA repair, and circadian rhythms. We report three crystal structures of the kinase domain of human CK1δ, one apo and two complexed with a potent and selective CK1δ/ε inhibitor PF670462 in two different crystal forms ...

    Casein kinase 1 delta (CK1δ) and its closest homologue CK1ε are key regulators of diverse cellular growth and survival processes such as Wnt signaling, DNA repair, and circadian rhythms. We report three crystal structures of the kinase domain of human CK1δ, one apo and two complexed with a potent and selective CK1δ/ε inhibitor PF670462 in two different crystal forms. These structures provide a molecular basis for the strong and specific inhibitor interactions and suggest clues for further development of CK1δ/ε inhibitors.


    Organizational Affiliation

    Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Casein kinase I isoform deltaA, B296Homo sapiensMutation(s): 0 
Gene Names: CSNK1DHCKID
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.26 (UniProt)
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0CK (Subject of Investigation/LOI)
Query on 0CK

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]4-[1-cyclohexyl-4-(4-fluorophenyl)-1H-imidazol-5-yl]pyrimidin-2-amine
C19 H20 F N5
WUDBUIUHVNECTM-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
0CK BindingDB:  3UZP IC50: min: 7.7, max: 130 (nM) from 12 assay(s)
PDBBind:  3UZP IC50: 13 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49α = 90
b = 72.8β = 103.21
c = 88.99γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2011-12-07 
  • Released Date: 2012-01-11 
  • Deposition Author(s): Huang, X.

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-11
    Type: Initial release
  • Version 1.1: 2012-11-14
    Changes: Database references