6RCG | pdb_00006rcg

Crystal structure of Casein kinase 1 delta (CK1 delta) complexed with SR3029 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6RCG/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-04-11 Released: 2020-03-25 
• Deposition Author(s): Chaikuad, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Roush, W.R., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Casein kinase 1 delta (CK1 delta) complexed with SR3029 inhibitor

Chaikuad, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Roush, W.R., Knapp, S., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.03 kDa 
• Atom Count: 2,915 
• Modelled Residue Count: 295 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase I isoform delta	A	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K0E	D [auth A]	~{N}-[[6,7-bis(fluoranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(3-fluorophenyl)-2-morpholin-4-yl-purin-6-amine C23 H19 F3 N8 O CEBMEQPREMCWOL-UHFFFAOYSA-N
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.04	α = 90
b = 53.55	β = 113.45
c = 72.17	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-25 
Deposition Author(s): Chaikuad, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Roush, W.R., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2020-03-25
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description