3FDN

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

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: 10.1021/jm801270e
  • Also Cited By: 3K5U

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase 6
A
279Homo sapiensMutation(s): 1 
Gene Names: AURKA (AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6)
EC: 2.7.11.1
Find proteins for O14965 (Homo sapiens)
Go to Gene View: AURKA
Go to UniProtKB:  O14965
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MMH
Query on MMH
Download SDF File 
Download CCD File 
A
N-[3-(acetylamino)phenyl]-5-{(2E)-2-[(4-methoxyphenyl)methylidene]hydrazino}-3-methyl-1H-pyrazole-4-carboxamide
(E)-N-(3-Acetamidophenyl)-5-(2-(4-methoxybenzylidene)hydrazinyl)-3-methyl-1H-pyrazole-4-carboxamide
C21 H22 N6 O3
NIZPETVEBKMXKW-WSDLNYQXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MMHIC50: 33 nM BINDINGMOAD
MMHIC50: 33 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.228 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 81.613α = 90.00
b = 81.613β = 90.00
c = 169.145γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
SCALEPACKdata scaling
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance