crystal structure of ck1d with PF670462 from P21 crystal form

Experimental Data Snapshot

  • Resolution: 1.94 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.222 

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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: https://doi.org/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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase I isoform delta
A, B
296Homo sapiensMutation(s): 0 
Gene Names: CSNK1D
UniProt & NIH Common Fund Data Resources
Find proteins for P48730 (Homo sapiens)
Explore P48730 
Go to UniProtKB:  P48730
GTEx:  ENSG00000141551 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48730
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0CK

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C19 H20 F N5
Binding Affinity Annotations 
IDSourceBinding Affinity
0CK BindingDB:  3UZP IC50: min: 7.7, max: 130 (nM) from 14 assay(s)
PDBBind:  3UZP IC50: 13 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • 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
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations