Crystal Structure of Aurora Kinase A in complex with N-{4-[(6-oxo-5,6-dihydrobenzo[c][1,8]naphthyridin-1-yl)amino]phenyl}benzamide

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.231 

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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

  • 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.

  • Organizational Affiliation

    EMD Serono Research Institute, Inc., 45A Middlesex Turnpike, Billerica, MA 01821, United States. Srinivasa.karra@emdserono.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase A284Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O14965 (Homo sapiens)
Explore O14965 
Go to UniProtKB:  O14965
PHAROS:  O14965
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14965
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on XU2

Download Ideal Coordinates CCD File 
B [auth A]N-{4-[(6-oxo-5,6-dihydrobenzo[c][1,8]naphthyridin-1-yl)amino]phenyl}benzamide
C25 H18 N4 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
XU2 PDBBind:  4JAI IC50: 4 (nM) from 1 assay(s)
BindingDB:  4JAI IC50: 4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.231 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.965α = 90
b = 83.965β = 90
c = 167.064γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

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