7QR9 | pdb_00007qr9

Crystal structure of CK1 delta in complex with PK-09-82


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.305 (Depositor), 0.309 (DCC) 
  • R-Value Work: 
    0.252 (Depositor), 0.259 (DCC) 
  • R-Value Observed: 
    0.254 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7QR9

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of Potent and Exquisitely Selective Inhibitors of Kinase CK1 with Tunable Isoform Selectivity.

Nemec, V.Khirsariya, P.Janovska, P.Moyano, P.M.Maier, L.Prochazkova, P.Kebkova, P.Gybel', T.Berger, B.T.Chaikuad, A.Reinecke, M.Kuster, B.Knapp, S.Bryja, V.Paruch, K.

(2023) Angew Chem Int Ed Engl 62: e202217532-e202217532

  • DOI: https://doi.org/10.1002/anie.202217532
  • Primary Citation Related Structures: 
    7QR9, 7QRA, 7QRB

  • PubMed Abstract: 

    Casein kinases 1 (CK1) are key signaling molecules that have emerged recently as attractive therapeutic targets in particular for the treatment of hematological malignancies. Herein, we report the identification of a new class of potent and highly selective inhibitors of CK1α, δ and ϵ. Based on their optimal in vitro and in vivo profiles and their exclusive selectivity, MU1250, MU1500 and MU1742 were selected as quality chemical probes for those CK1 isoforms. At proper concentrations, MU1250 and MU1500 allow for specific targeting of CK1δ or dual inhibition of CK1δ/ϵ in cells. The compound MU1742 also efficiently inhibits CK1α and, to our knowledge, represents the first potent and highly selective inhibitor of this enzyme. In addition, we demonstrate that the central 1H-pyrrolo[2,3-b]pyridine-imidazole pharmacophore can be used as the basis of highly selective inhibitors of other therapeutically relevant protein kinases, e.g. p38α, as exemplified by the compound MU1299.


  • Organizational Affiliation
    • Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 140.57 kDa 
  • Atom Count: 9,847 
  • Modeled Residue Count: 1,146 
  • Deposited Residue Count: 1,184 
  • 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
296Homo 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
EZQ
(Subject of Investigation/LOI)

Query on EZQ



Download:Ideal Coordinates CCD File
P [auth A],
T [auth B],
W [auth C],
Z [auth D]
4-[5-(4-fluorophenyl)-3-(pyridin-4-ylmethyl)imidazol-4-yl]-1~{H}-pyrrolo[2,3-b]pyridine
C22 H16 F N5
RJSIBZBOEOZVIR-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
Q [auth B]
R [auth B]
U [auth C]
E [auth A],
F [auth A],
Q [auth B],
R [auth B],
U [auth C],
V [auth C],
X [auth D],
Y [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
S [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.305 (Depositor), 0.309 (DCC) 
  • R-Value Work:  0.252 (Depositor), 0.259 (DCC) 
  • R-Value Observed: 0.254 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.438α = 70.27
b = 85.24β = 74.1
c = 89.678γ = 86.86
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-18
    Type: Initial release
  • Version 1.1: 2023-04-19
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description