4KBA

CK1d in complex with 9-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]-2,3,4,5-tetrahydropyrido[2,3-f][1,4]oxazepine inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Ligand-protein interactions of selective casein kinase 1 delta inhibitors.

Mente, S., Arnold, E., Butler, T., Chakrapani, S., Chandrasekaran, R., Cherry, K., Dirico, K., Doran, A., Fisher, K., Galatsis, P., Green, M., Hayward, M., Humphrey, J., Knafels, J., Li, J., Liu, S., Marconi, M., McDonald, S., Ohren, J., Paradis, V., Sneed, B., Walton, K., Wager, T.

(2013) J Med Chem 56: 6819-6828

  • DOI: 10.1021/jm4006324
  • Primary Citation of Related Structures:  
    4KB8, 4KBA, 4KBC, 4KBK

  • PubMed Abstract: 

    • Casein kinase 1δ (CK1δ) and 1ε (CK1ε) are believed to be necessary enzymes for the regulation of circadian rhythms in all mammals. On the basis of our previously published work demonstrating a CK1ε-preferring compound to be an ineffective circadian clock modulator, we have synthesized a series of pyrazole-substitued pyridine inhibitors, selective for the CK1δ isoform ...

    Casein kinase 1δ (CK1δ) and 1ε (CK1ε) are believed to be necessary enzymes for the regulation of circadian rhythms in all mammals. On the basis of our previously published work demonstrating a CK1ε-preferring compound to be an ineffective circadian clock modulator, we have synthesized a series of pyrazole-substitued pyridine inhibitors, selective for the CK1δ isoform. Additionally, using structure-based drug design, we have been able to exploit differences in the hinge region between CK1δ and p38 to find selective inhibitors that have minimal p38 activity. The SAR, brain exposure, and the effect of these inhibitors on mouse circadian rhythms are described. The in vivo evaluation of these inhibitors demonstrates that selective inhibition of CK1δ at sufficient central exposure levels is capable of modulating circadian rhythms.

    Organizational Affiliation: 

    Pfizer Worldwide Research and Development , 700 Main Street, Cambridge, Massachusetts 02139, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Casein kinase I isoform deltaA, B, C, D331Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48730
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
1QM PDBBind:  4KBA IC50: 6 (nM) from 1 assay(s)
BindingDB:  4KBA IC50: min: 6, max: 42 (nM) from 3 assay(s)
Binding MOAD:  4KBA IC50: 6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.689α = 108
b = 83.964β = 105.71
c = 89.29γ = 93
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2013-04-23 
  • Released Date: 2013-09-18 
    • Deposition Author(s): Liu, S.

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-09-25
    Changes: Database references