8VXF | pdb_00008vxf

Structure of Casein kinase I isoform delta (CK1d) complexed with inhibitor 15

• PDB DOI: https://doi.org/10.2210/pdb8VXF/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-02-04 Released: 2024-05-08 
• Deposition Author(s): Thompson, A.A., Milligan, C.M., Sharma, S.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.271 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Structure-Based Optimization of Selective and Brain Penetrant CK1 delta Inhibitors for the Treatment of Circadian Disruptions.

McCarver, S., Hanna, L., Samant, A., Thompson, A.A., Seierstad, M., Saha, A., Wu, D., Lord, B., Sutton, S.W., Shah, V., Milligan, C.M., Wennerholm, M., Shelton, J., Lebold, T.P., Shireman, B.T.

(2024) ACS Med Chem Lett 15: 486-492

• PubMed: 38628796 
• DOI: https://doi.org/10.1021/acsmedchemlett.3c00523
• Primary Citation Related Structures: 
  8VXD, 8VXE, 8VXF


• PubMed Abstract: 
  

  Neuropsychiatric disorders such as major depressive disorders and schizophrenia are often associated with disruptions to the normal 24 h sleep wake cycle. Casein kinase 1 (CK1δ) is an integral part of the molecular machinery that regulates circadian rhythms. Starting from a cluster of bicyclic pyrazoles identified from a virtual screening effort, we utilized structure-based drug design to identify and reinforce a unique "hinge-flip" binding mode that provides a high degree of selectivity for CK1δ versus the kinome. Pharmacokinetics, brain exposure, and target engagement as measured by ex vivo autoradiography are described for advanced analogs.

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Organizational Affiliation: 
• Janssen Research and Development, San Diego, California 92121-1126, United States.

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: 70.31 kDa 
• Atom Count: 4,646 
• Modeled Residue Count: 578 
• Deposited Residue Count: 600 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase I isoform delta	A	300	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase I isoform delta	B	300	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
A1AD8 (Subject of Investigation/LOI)	C [auth A], D [auth B]	(2P,3P,8S)-2-(5-fluoropyridin-2-yl)-6,6-dimethyl-3-(1H-pyrazolo[3,4-b]pyridin-4-yl)-6,7-dihydro-4H-pyrazolo[5,1-c][1,4]oxazine C19 H17 F N6 O WZMIWVZGYMKUDV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.271 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.127	α = 90
b = 100.891	β = 101.85
c = 65.958	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-08 
Deposition Author(s): Thompson, A.A., Milligan, C.M., Sharma, S.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Structure summary