3U4U

Casein kinase 2 in complex with AZ-Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3U4U/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-10-10 Released: 2012-08-22 
• Deposition Author(s): Larsen, N.A., Dowling, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.269 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Literature

Potent and Selective Inhibitors of CK2 Kinase Identified through Structure-Guided Hybridization.

Dowling, J.E., Chuaqui, C., Pontz, T.W., Lyne, P.D., Larsen, N.A., Block, M.H., Chen, H., Su, N., Wu, A., Russell, D., Pollard, H., Lee, J.W., Peng, B., Thakur, K., Ye, Q., Zhang, T., Brassil, P., Racicot, V., Bao, L., Denz, C.R., Cooke, E.

(2012) ACS Med Chem Lett 3: 278-283

• PubMed: 24900464 
• DOI: https://doi.org/10.1021/ml200257n
• Primary Citation of Related Structures:  
  3U4U


• PubMed Abstract: 
  

  In this paper we describe a series of 3-cyano-5-aryl-7-aminopyrazolo[1,5-a]pyrimidine hits identified by kinase-focused subset screening as starting points for the structure-based design of conformationally constrained 6-acetamido-indole inhibitors of CK2. The synthesis, SAR, and effects of this novel series on Akt signaling and cell proliferation in vitro are described.

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Organizational Affiliation: 

AstraZeneca , Oncology Innovative Medicines Unit, 35 Gatehouse Drive, Waltham, Massachusetts 02145, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.36 kDa 
• Atom Count: 2,934 
• Modelled Residue Count: 327 
• Deposited Residue Count: 333 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A	333	Homo sapiens	Mutation(s): 0  Gene Names: CSNK2A1, CK2A1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P68400 (Homo sapiens) Explore P68400  Go to UniProtKB:  P68400
PHAROS:  P68400 GTEx:  ENSG00000101266

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LNH	B [auth A]	3-{5-(acetylamino)-3-[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]-1H-indol-1-yl}propanoic acid C23 H21 N7 O3 FXZDYVDTIVZZCX-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
LNH	BindingDB:  3U4U	IC50: min: 3, max: 3100 (nM) from 2 assay(s)
	PDBBind:  3U4U	IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.269 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.528	α = 90
b = 61.895	β = 90
c = 116.064	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-22 
Deposition Author(s): Larsen, N.A., Dowling, J.

Revision History  

• Version 1.0: 2012-08-22
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations