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 

wwPDB Validation 3D Report Full Report


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, 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 c ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase I isoform delta
A, B, C, D
331Homo sapiensGene Names: CSNK1D (HCKID)
EC: 2.7.11.1, 2.7.11.26
Find proteins for P48730 (Homo sapiens)
Go to Gene View: CSNK1D
Go to UniProtKB:  P48730
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
1QM
Query on 1QM

Download SDF File 
Download CCD File 
A, B, C, D
9-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]-2,3,4,5-tetrahydropyrido[2,3-f][1,4]oxazepine
C18 H17 F N4 O
RDUXJEGWTNOYDA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1QMIC50: 6 - 42 nM (100) BINDINGDB
1QMIC50: 654 nM BINDINGMOAD
1QMIC50: 6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.208 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 48.689α = 108.00
b = 83.964β = 105.71
c = 89.290γ = 93.00
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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