5W4W | pdb_00005w4w

Identification and Profiling of a Selective and Brain Penetrant Radioligand for In Vivo Target Occupancy Measurement of Casein Kinase 1 (CK1) Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.215 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.180 (Depositor) 
  • R-Value Observed: 
    0.181 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5W4W

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Identification and Profiling of a Selective and Brain Penetrant Radioligand for in Vivo Target Occupancy Measurement of Casein Kinase 1 (CK1) Inhibitors.

Wager, T.T.Galatsis, P.Chandrasekaran, R.Y.Butler, T.W.Li, J.Zhang, L.Mente, S.Subramanyam, C.Liu, S.Doran, A.C.Chang, C.Fisher, K.Grimwood, S.Hedde, J.R.Marconi, M.Schildknegt, K.

(2017) ACS Chem Neurosci 8: 1995-2004

  • DOI: https://doi.org/10.1021/acschemneuro.7b00155
  • Primary Citation Related Structures: 
    5W4W

  • PubMed Abstract: 

    To enable the clinical development of our CNS casein kinase 1 delta/epsilon (CK1δ/ε) inhibitor project, we investigated the possibility of developing a CNS positron emission tomography (PET) radioligand. For this effort, we focused our design and synthesis efforts on the initial CK1δ/ε inhibitor HTS hits with the goal of identifying a compound that would fulfill a set of recommended PET ligand criteria. We identified [ 3 H]PF-5236216 (9) as a tool ligand that meets most of the key CNS PET attributes including high CNS MPO PET desirability score and kinase selectivity, CNS penetration, and low nonspecific binding. We further used [ 3 H]-9 to determine the binding affinity for PF-670462, a literature CK1δ/ε inhibitor tool compound. Lastly, [ 3 H]-9 was used to measure in vivo target occupancy (TO) of PF-670462 in mouse and correlated TO with CK1δ/ε in vivo pharmacology (circadian rhythm modulation).


  • Organizational Affiliation
    • Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , 1 Portland, Cambridge, Massachusetts 02139, United States.

Macromolecule Content 

  • Total Structure Weight: 156.88 kDa 
  • Atom Count: 10,124 
  • Modeled Residue Count: 1,153 
  • 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9WG

Query on 9WG



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
P [auth C],
U [auth D]
4-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]-6-methyl-6,7-dihydro-5H-pyrrolo[3,4-b]pyridin-5-one
C18 H15 F N4 O
NGDXEOHYWJHBTJ-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
J [auth B]
K [auth B]
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
V [auth D],
W [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.215 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.180 (Depositor) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.884α = 70.37
b = 84.584β = 74.27
c = 89.042γ = 86.77
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2017-06-28 
  • Deposition Author(s): Liu, S.

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-10-04
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references