Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.77 kDa 
• Atom Count: 2363 
• Modelled Residue Count: 261 
• Deposited Residue Count: 279 
• Unique protein chains: 1

3FDN

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

• PDB DOI: 10.2210/pdb3FDN/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2008-11-26 Released: 2009-09-15 
• Deposition Author(s): Leou, J.S., Wu, J.S., Coumar, M.S., Shukla, P., Hsieh, H.P., Wu, S.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.287 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 

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

• PubMed: 19140666 
• DOI: 10.1021/jm801270e
• Primary Citation of Related Structures:  
  3FDN


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase 6	A	279	Homo sapiens	Mutation(s): 1  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
PHAROS:  O14965 GTEx:  ENSG00000087586

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MMH	B [auth A]	N-[3-(acetylamino)phenyl]-5-{(2E)-2-[(4-methoxyphenyl)methylidene]hydrazino}-3-methyl-1H-pyrazole-4-carboxamide C21 H22 N6 O3 NIZPETVEBKMXKW-WSDLNYQXSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MMH	Binding MOAD:  3FDN	IC50: 33 (nM) from 1 assay(s)
	PDBBind:  3FDN	IC50: 33 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 81.613	α = 90
b = 81.613	β = 90
c = 169.145	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-11-26 
• Released Date: 2009-09-15 
Deposition Author(s): Leou, J.S., Wu, J.S., Coumar, M.S., Shukla, P., Hsieh, H.P., Wu, S.Y.

Revision History  

• 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