Crystal Structure of Aurora A Kinase complexed with inhibitor

Experimental Data Snapshot

  • Resolution: 2.75 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.221 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Fast-forwarding hit to lead: aurora and epidermal growth factor receptor kinase inhibitor lead identification

Coumar, M.S.Chu, C.Y.Lin, C.W.Shiao, H.Y.Ho, Y.L.Reddy, R.Lin, W.H.Chen, C.H.Peng, Y.H.Leou, J.S.Lien, T.W.Huang, C.T.Fang, M.Y.Wu, S.H.Wu, J.S.Chittimalla, S.K.Song, J.S.Hsu, J.T.Wu, S.Y.Liao, C.C.Chao, Y.S.Hsieh, H.P.

(2010) J Med Chem 53: 4980-4988

  • DOI: https://doi.org/10.1021/jm1000198
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A focused library of furanopyrimidine (350 compounds) was rapidly synthesized in parallel reactors and in situ screened for Aurora and epidermal growth factor receptor (EGFR) kinase activity, leading to the identification of some interesting hits. On the basis of structural biology observations, the hit 1a was modified to better fit the back pocket, producing the potent Aurora inhibitor 3 with submicromolar antiproliferative activity in HCT-116 colon cancer cell line. On the basis of docking studies with EGFR hit 1s, introduction of acrylamide Michael acceptor group led to 8, which inhibited both the wild and mutant EGFR kinase and also showed antiproliferative activity in HCC827 lung cancer cell line. Furthermore, the X-ray cocrystal study of 3 and 8 in complex with Aurora and EGFR, respectively, confirmed their hypothesized binding modes. Library construction, in situ screening, and structure-based drug design (SBDD) strategy described here could be applied for the lead identification of other kinases.

  • Organizational Affiliation

    Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase 6279Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for O14965 (Homo sapiens)
Explore O14965 
Go to UniProtKB:  O14965
PHAROS:  O14965
GTEx:  ENSG00000087586 
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 AKI

Download Ideal Coordinates CCD File 
B [auth A]1-(4-{2-[(5,6-diphenylfuro[2,3-d]pyrimidin-4-yl)amino]ethyl}phenyl)-3-phenylurea
C33 H27 N5 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
AKI PDBBind:  3M11 IC50: 43 (nM) from 1 assay(s)
BindingDB:  3M11 IC50: 43 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.75 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.221 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.266α = 90
b = 82.266β = 90
c = 170.283γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description