4HNI

crystal structure of ck1e in complex with PF4800567

• PDB DOI: https://doi.org/10.2210/pdb4HNI/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-19 Released: 2012-11-14 
• Deposition Author(s): Huang, X., Long, A.M., Zhao, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 0.273 
• R-Value Work: 0.237 

Literature

Structural basis for the potent and selective inhibition of casein kinase 1 epsilon.

Long, A.M., Zhao, H., Huang, X.

(2012) J Med Chem 55: 10307-10311

• PubMed: 23106386 
• DOI: https://doi.org/10.1021/jm301336n
• Primary Citation of Related Structures:  
  4HNF, 4HNI, 4HOK


• PubMed Abstract: 
  

  Casein kinase 1 epsilon (CK1ε) and its closest homologue CK1δ are key regulators of diverse cellular processes. We report two crystal structures of PF4800567, a potent and selective inhibitor of CK1ε, bound to the kinase domains of human CK1ε and CK1δ as well as one apo CK1ε crystal structure. These structures provide a molecular basis for the strong and specific inhibitor interactions with CK1ε and suggest clues for further development of CK1δ inhibitors.

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Organizational Affiliation: 

Department of Molecular Structure and Characterization, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 70.22 kDa 
• Atom Count: 4,755 
• Modelled Residue Count: 568 
• Deposited Residue Count: 592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase I isoform epsilon	A, B	296	Homo sapiens	Mutation(s): 0  Gene Names: CSNK1E EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49674 (Homo sapiens) Explore P49674  Go to UniProtKB:  P49674
PHAROS:  P49674 GTEx:  ENSG00000213923

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
16W	C [auth A], I [auth B]	3-[(3-chlorophenoxy)methyl]-1-(tetrahydro-2H-pyran-4-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine C17 H18 Cl N5 O2 AUMDBEHGJRZSOO-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
16W	PDBBind:  4HNI	IC50: 32 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 0.273 
• R-Value Work: 0.237 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.108	α = 90
b = 111.108	β = 90
c = 155.426	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Huang, X., Long, A.M., Zhao, H.

Revision History  

• Version 1.0: 2012-11-14
  Type: Initial release
  
• Version 1.1: 2013-01-02
  Changes: Database references
• Version 1.2: 2018-11-07
  Changes: Data collection, Experimental preparation
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations