4TN6 | pdb_00004tn6

CK1d in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4TN6/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-06-03 Released: 2015-08-12 
• Deposition Author(s): Liu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

CK1D IN COMPLEX WITH inhibitor

Liu, S.

To be published.

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.

Macromolecule Content 

• Total Structure Weight: 74.42 kDa 
• Atom Count: 5,001 
• Modeled Residue Count: 577 
• Deposited Residue Count: 636 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase I isoform delta	A, B	318	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PFO	C [auth A]	4-{4-(4-fluorophenyl)-1-[1-(1,2-oxazol-3-ylmethyl)piperidin-4-yl]-1H-imidazol-5-yl}pyrimidin-2-amine C22 H22 F N7 O XPWHRQHBPRSUAW-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
PFO	BindingDB:  4TN6	IC50: min: 3.9, max: 17 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.487	α = 90
b = 115.336	β = 109.27
c = 61.533	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-12 
Deposition Author(s): Liu, S.

Revision History  

• Version 1.0: 2015-08-12
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description