2XNE | pdb_00002xne

Structure of Aurora-A bound to an imidazopyrazine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2XNE/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-08-02 Released: 2010-09-22 
• Deposition Author(s): Kosmopoulou, M., Bayliss, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Structure-based design of imidazo[1,2-a]pyrazine derivatives as selective inhibitors of Aurora-A kinase in cells.

Bouloc, N., Large, J.M., Kosmopoulou, M., Sun, C., Faisal, A., Matteucci, M., Reynisson, J., Brown, N., Atrash, B., Blagg, J., McDonald, E., Linardopoulos, S., Bayliss, R., Bavetsias, V.

(2010) Bioorg Med Chem Lett 20: 5988-5993

• PubMed: 20833547 
• DOI: https://doi.org/10.1016/j.bmcl.2010.08.091
• Primary Citation of Related Structures:  
  2XNE, 2XNG


• PubMed Abstract: 
  

  Co-crystallisation of the imidazo[1,2-a]pyrazine derivative 15 (3-chloro-N-(4-morpholinophenyl)-6-(pyridin-3-yl)imidazo[1,2-a]pyrazin-8-amine) with Aurora-A provided an insight into the interactions of this class of compound with Aurora kinases. This led to the design and synthesis of potent Aurora-A inhibitors demonstrating up to 70-fold selectivity in cell-based Aurora kinase pharmacodynamic biomarker assays.

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Organizational Affiliation: 

Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, Sutton, Surrey, United Kingdom.

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: 32.03 kDa 
• Atom Count: 1,951 
• Modelled Residue Count: 246 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE 6	A	272	Homo sapiens	Mutation(s): 1  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
ASH	B [auth A]	3-chloro-N-(4-morpholin-4-ylphenyl)-6-pyridin-3-ylimidazo[1,2-a]pyrazin-8-amine C21 H19 Cl N6 O FXFAGYZXIGMEEG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ASH	BindingDB:  2XNE	IC50: 190 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.923	α = 90
b = 82.923	β = 90
c = 167.092	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Kosmopoulou, M., Bayliss, R.

Revision History  

• Version 1.0: 2010-09-22
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-02-28
  Changes: Database references
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description