4KB8

CK1d in complex with 1-{4-[3-(4-FLUOROPHENYL)-1-METHYL-1H-PYRAZOL-4-YL]PYRIDIN-2-YL}-N-METHYLMETHANAMINE ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

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:  
    4KBC, 4KBA, 4KB8, 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Casein kinase I isoform deltaABCD331Homo sapiensMutation(s): 0 
Gene Names: CSNK1DHCKID
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.26 (PDB Primary Data)
Find proteins for P48730 (Homo sapiens)
Explore P48730 
Go to UniProtKB:  P48730
NIH Common Fund Data Resources
PHAROS  P48730
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1QN
Query on 1QN

Download CCD File 
A, C
1-{4-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]pyridin-2-yl}-N-methylmethanamine
C17 H17 F N4
UEPOHWWKVBWCFV-UHFFFAOYSA-N
 Ligand Interaction
1QO
Query on 1QO

Download CCD File 
B, D
N-benzyl-4-(pyridin-3-yl)pyrimidin-2-amine
C16 H14 N4
JTYLHRZXSYVYMO-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1QNIC50 :  12.899999618530273   nM  PDBBind
1QNIC50:  3040   nM  Binding MOAD
1QNIC50:  13   nM  BindingDB
1QNIC50:  67   nM  BindingDB
1QNIC50:  64   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.014α = 107.9
b = 84.541β = 105.87
c = 89.515γ = 93.08
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

View Full Validation Report



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
    Changes: Database references