4HNF | pdb_00004hnf

Crystal structure of ck1d in complex with pf4800567

• PDB DOI: https://doi.org/10.2210/pdb4HNF/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: 2.07 Å
• R-Value Free: 
  0.274 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.230 (DCC) 

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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69.42 kDa 
• Atom Count: 5,032 
• Modelled Residue Count: 579 
• Deposited Residue Count: 592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase I isoform delta	A, B	296	Homo sapiens	Mutation(s): 0  Gene Names: CSNK1D, HCKID 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 GTEx:  ENSG00000141551

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
16W	C [auth A], D [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

Binding Affinity Annotations
ID	Source	Binding Affinity
16W	BindingDB:  4HNF	IC50: min: 32, max: 711 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.274 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.230 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.217	α = 90
b = 48.109	β = 110.67
c = 80.467	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: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations