3VAP

Synthesis and SAR Studies of imidazo-[1,2-a]-pyrazine Aurora kinase inhibitors with improved off target kinase selectivity

• PDB DOI: https://doi.org/10.2210/pdb3VAP/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-12-29 Released: 2012-05-02 
• Deposition Author(s): Voss, M.E., Rainka, M.P., Fleming, M., Peterson, L.H., Belanger, D.B., Siddiqui, M.A., Hruza, A., Voigt, J., Basso, A.D., Gray, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.246 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

Literature

Synthesis and SAR studies of imidazo-[1,2-a]-pyrazine Aurora kinase inhibitors with improved off-target kinase selectivity.

Voss, M.E., Rainka, M.P., Fleming, M., Peterson, L.H., Belanger, D.B., Siddiqui, M.A., Hruza, A., Voigt, J., Gray, K., Basso, A.D.

(2012) Bioorg Med Chem Lett 22: 3544-3549

• PubMed: 22503250 
• DOI: https://doi.org/10.1016/j.bmcl.2012.03.051
• Primary Citation of Related Structures:  
  3VAP


• PubMed Abstract: 
  

  The structure-activity relationships of new Aurora A/B kinase inhibitors derived from the previously identified kinase inhibitor 12 are described. Introduction of acetic acid amides onto the pyrazole of compound 12 was postulated to influence Aurora A/B selectivity and improve the profile against off-target kinases. The SAR of the acetic acid amides was explored and the effect of substitution on enzyme inhibition as well as mechanism-based cell activity was studied. Additionally, several of the more potent inhibitors were screened for their off-target kinase selectivity.

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Organizational Affiliation: 

AMRI Global, 26 Corporate Circle, Albany, NY 12212, USA. [e-mail]

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: 32 kDa 
• Atom Count: 2,091 
• Modelled Residue Count: 249 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aurora kinase A	A	272	Homo sapiens	Mutation(s): 0  Gene Names: AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14965 (Homo sapiens) Explore O14965  Go to UniProtKB:  O14965
PHAROS:  O14965 GTEx:  ENSG00000087586

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0FY	B [auth A]	3-(1-{2-[(3-fluoropyridinium-4-yl)amino]-2-oxoethyl}-1H-pyrazol-4-yl)-6-methyl-8-[(3-{[(1R,3R)-3-methylpiperidinium-1-yl]methyl}-1,2-thiazol-5-yl)amino]imidazo[1,2-a]pyrazin-1-ium C27 H32 F N10 O S PBHYAPKEUOBQSL-QGZVFWFLSA-Q

Binding Affinity Annotations
ID	Source	Binding Affinity
0FY	PDBBind:  3VAP	IC50: 4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.246 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.329	α = 90
b = 83.329	β = 90
c = 157.7	γ = 120

Software Package:

Software Name	Purpose
StructureStudio	data collection
BUSTER	refinement
autoPROC	data scaling
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-02 
Deposition Author(s): Voss, M.E., Rainka, M.P., Fleming, M., Peterson, L.H., Belanger, D.B., Siddiqui, M.A., Hruza, A., Voigt, J., Basso, A.D., Gray, K.

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2012-05-23
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Refinement description