Structure-based drug design of novel Aurora kinase A inhibitors: Structure basis for potency and specificity

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report

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Structure-based drug design of novel Aurora kinase A inhibitors: structural basis for potency and specificity

Coumar, M.S.Leou, J.S.Shukla, P.Wu, J.S.Dixit, A.K.Lin, W.H.Chang, C.Y.Lien, T.W.Tan, U.K.Chen, C.H.Hsu, J.T.A.Chao, Y.S.Wu, S.Y.Hsieh, H.P.

(2009) J Med Chem 52: 1050-1062

  • DOI: https://doi.org/10.1021/jm801270e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Aurora kinases have emerged as attractive targets for the design of anticancer drugs. Through structure-based virtual screening, novel pyrazole hit 8a was identified as Aurora kinase A inhibitor (IC(50) = 15.1 microM). X-ray cocrystal structure of 8a in complex with Aurora A protein revealed the C-4 position ethyl carboxylate side chain as a possible modification site for improving the potency. On the basis of this insight, bioisosteric replacement of the ester with amide linkage and changing the ethyl substituent to hydrophobic 3-acetamidophenyl ring led to the identification of 12w with a approximately 450-fold improved Aurora kinase A inhibition potency (IC(50) = 33 nM), compared to 8a. Compound 12w showed selective inhibition of Aurora A kinase over Aurora B/C, which might be due to the presence of a unique H-bond interaction between the 3-acetamido group and the Aurora A nonconserved Thr217 residue, which in Aurora B/C is Glu and found to sterically clash with the 3-acetamido group in modeling studies.

  • 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
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 MMH

Download Ideal Coordinates CCD File 
B [auth A]N-[3-(acetylamino)phenyl]-5-{(2E)-2-[(4-methoxyphenyl)methylidene]hydrazino}-3-methyl-1H-pyrazole-4-carboxamide
C21 H22 N6 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
MMH PDBBind:  3FDN IC50: 33 (nM) from 1 assay(s)
Binding MOAD:  3FDN IC50: 33 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.613α = 90
b = 81.613β = 90
c = 169.145γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description