CK1d in complex with (3S)-3-{4-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]pyridin-2-yl}morpholine inhibitor

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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: https://doi.org/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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase I isoform delta
A, B, C, D
331Homo sapiensMutation(s): 0 
EC: (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P48730 (Homo sapiens)
Explore P48730 
Go to UniProtKB:  P48730
GTEx:  ENSG00000141551 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48730
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1QG

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
N [auth C],
R [auth D]
C19 H19 F N4 O
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
K [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
Q [auth C],
S [auth D],
T [auth D],
U [auth D]
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
1QG BindingDB:  4KBK IC50: min: 6.6, max: 90 (nM) from 3 assay(s)
PDBBind:  4KBK IC50: 6.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.103α = 108.06
b = 84.76β = 105.85
c = 89.447γ = 93.09
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • 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
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations