4KB8 | pdb_00004kb8

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 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4KB8

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/jm4006324
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 156.03 kDa 
  • Atom Count: 9,385 
  • Modeled Residue Count: 1,105 
  • Deposited Residue Count: 1,324 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Casein kinase I isoform delta
A, B, C, D
331Homo sapiensMutation(s): 0 
Gene Names: CSNK1DHCKID
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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1QN

Query on 1QN



Download:Ideal Coordinates CCD File
E [auth A],
K [auth C]
1-{4-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]pyridin-2-yl}-N-methylmethanamine
C17 H17 F N4
UEPOHWWKVBWCFV-UHFFFAOYSA-N
1QO

Query on 1QO



Download:Ideal Coordinates CCD File
H [auth B],
N [auth D]
N-benzyl-4-(pyridin-3-yl)pyrimidin-2-amine
C16 H14 N4
JTYLHRZXSYVYMO-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
I [auth B]
J [auth B]
L [auth C]
F [auth A],
G [auth A],
I [auth B],
J [auth B],
L [auth C],
M [auth C],
O [auth D],
P [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.232 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
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



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