4HNI

crystal structure of ck1e in complex with PF4800567


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase I isoform epsilon
A, B
296Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49674
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
16W
Query on 16W

Download Ideal Coordinates CCD File 
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
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
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 
IDSourceBinding Affinity
16W BindingDB:  4HNI IC50: min: 32, max: 711 (nM) from 3 assay(s)
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 = 111.108α = 90
b = 111.108β = 90
c = 155.426γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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