4JAJ

Crystal Structure of Aurora Kinase A in complex with BENZO[C][1,8]NAPHTHYRIDIN-6(5H)-ONE

• PDB DOI: https://doi.org/10.2210/pdb4JAJ/pdb

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


• Deposited: 2013-02-18 Released: 2013-05-22 
• Deposition Author(s): Jiang, X., Josephson, K., Huck, B., Goutopoulos, A., Karra, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.323 
• R-Value Work: 0.232 
• R-Value Observed: 0.238 

Starting Model: experimental

Literature

SAR and evaluation of novel 5H-benzo[c][1,8]naphthyridin-6-one analogs as Aurora kinase inhibitors.

Karra, S., Xiao, Y., Chen, X., Liu-Bujalski, L., Huck, B., Sutton, A., Goutopoulos, A., Askew, B., Josephson, K., Jiang, X., Shutes, A., Shankar, V., Noonan, T., Garcia-Berrios, G., Dong, R., Dhanabal, M., Tian, H., Wang, Z., Clark, A., Goodstal, S.

(2013) Bioorg Med Chem Lett 23: 3081-3087

• PubMed: 23570792 
• DOI: https://doi.org/10.1016/j.bmcl.2013.03.008
• Primary Citation of Related Structures:  
  4JAI, 4JAJ


• PubMed Abstract: 
  

  Several potent Aurora kinase inhibitors derived from 5H-benzo[c][1,8]naphthyridin-6-one scaffold were identified. A crystal structure of Aurora kinase A in complex with an initial hit revealed a binding mode of the inhibitor within the ATP binding site and provided insight for structure-guided compound optimization. Subsequent SAR campaign provided a potent and selective pan Aurora inhibitor, which demonstrated potent target modulation and antiproliferative effects in the pancreatic cell line, MIAPaCa-2. Furthermore, this compound inhibited phosphorylation of histone H3 (pHH3) in mouse bone morrow upon oral administration, which is consistent with inhibition of Aurora kinase B activity.

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Organizational Affiliation: 

EMD Serono Research Institute, Inc., 45A Middlesex Turnpike, Billerica, MA 01821, United States. [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: 33.24 kDa 
• Atom Count: 2,189 
• Modelled Residue Count: 265 
• Deposited Residue Count: 284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aurora kinase A	A	284	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
GTEx:  ENSG00000087586

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XU1	B [auth A]	benzo[c][1,8]naphthyridin-6(5H)-one C12 H8 N2 O YLSBDRGLLZDAKB-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
XU1	BindingDB:  4JAJ	IC50: 5540 (nM) from 1 assay(s)
	PDBBind:  4JAJ	IC50: 5540 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.323 
• R-Value Work: 0.232 
• R-Value Observed: 0.238 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.841	α = 90
b = 81.841	β = 90
c = 169.44	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-22 
Deposition Author(s): Jiang, X., Josephson, K., Huck, B., Goutopoulos, A., Karra, S.

Revision History  

• Version 1.0: 2013-05-22
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description