4TW9

Difluoro-dioxolo-benzoimidazol-benzamides as potent inhibitors of CK1delta and epsilon with nanomolar inhibitory activity on cancer cell proliferation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.210 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Difluoro-dioxolo-benzoimidazol-benzamides As Potent Inhibitors of CK1 delta and epsilon with Nanomolar Inhibitory Activity on Cancer Cell Proliferation.

Richter, J.Bischof, J.Zaja, M.Kohlhof, H.Othersen, O.Vitt, D.Alscher, V.Pospiech, I.Garcia-Reyes, B.Berg, S.Leban, J.Knippschild, U.

(2014) J Med Chem 57: 7933-7946

  • DOI: https://doi.org/10.1021/jm500600b
  • Primary Citation of Related Structures:  
    4TW9

  • PubMed Abstract: 

    Deregulation of CK1 (casein kinase 1) activity can be involved in the development of several pathological disorders and diseases such as cancer. Therefore, research interest in identifying potent CK1-specific inhibitors is still increasing. A previously published potent and selective benzimidazole-derived CK1δ/ε-specific inhibitor compound with significant effects on several tumor cell lines was further modified to difluoro-dioxolo-benzoimidazole derivatives displaying remarkable inhibitory effects and increased intracellular availability. In the present study, we identified two heterocyclic molecules as new CK1-specific inhibitor compounds with favorable physicochemical properties and notable selectivity in a kinome-wide screen. Being compared to other CK1 isoforms, these compounds exhibited advanced isoform selectivity toward CK1δ. Moreover, newly designed compounds showed increased growth inhibitory activity in a panel of different tumor cell lines as determined by analyses of cell viability and cell cycle distribution. In summary, presented lead optimization resulted in new highly selective CK1δ-specific small molecule inhibitors with increased biological activity.


  • Organizational Affiliation

    Department of General and Visceral Surgery, Ulm University Hospital , Albert-Einstein-Allee 23, D-89081 Ulm, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase I isoform delta
A, B
295Homo sapiensMutation(s): 1 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
386
Query on 386

Download Ideal Coordinates CCD File 
L [auth A],
T [auth B]
N-(2,2-difluoro-5H-[1,3]dioxolo[4,5-f]benzimidazol-6-yl)-2-{[2-(trifluoromethoxy)benzoyl]amino}-1,3-thiazole-4-carboxamide
C20 H10 F5 N5 O5 S
DVVVOLSRHWJCHV-UHFFFAOYSA-N
HSJ
Query on HSJ

Download Ideal Coordinates CCD File 
G [auth A],
M [auth A]
octyl beta-L-talopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-MRTXSQPYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
N [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
R [auth B],
S [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
386 BindingDB:  4TW9 IC50: min: 10, max: 8.01e+4 (nM) from 9 assay(s)
Binding MOAD:  4TW9 IC50: 20 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.049α = 90
b = 135.707β = 99.42
c = 57.183γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 1.2: 2014-10-22
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations