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 4TW9 | pdb_00004tw9

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 (Depositor), 0.308 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4TW9

Ligand Structure Quality Assessment 


This is version 2.1 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 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.

Macromolecule Content 

  • Total Structure Weight: 71.19 kDa 
  • Atom Count: 5,149 
  • Modeled Residue Count: 579 
  • Deposited Residue Count: 590 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Casein kinase I isoform delta
A, B
295Homo sapiensMutation(s): 1 
Gene Names: CSNK1D, HCKID
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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.298 (Depositor), 0.308 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
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

View Full Validation Report



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
  • Version 2.1: 2024-05-08
    Changes: Data collection, Database references, Structure summary