Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 32.88 kDa 
• Atom Count: 2202 
• Modelled Residue Count: 256 
• Deposited Residue Count: 279 
• Unique protein chains: 1

3M11

Crystal Structure of Aurora A Kinase complexed with inhibitor

• DOI: 10.2210/pdb3M11/pdb

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


• Deposited: 2010-03-03 Released: 2011-03-09 
• Deposition Author(s): Wu, J.S., Leou, J.S., Coumar, M.S., Hsieh, H.P., Wu, S.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.299 
• R-Value Work: 0.217 
• R-Value Observed: 0.221 

Literature

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

• PubMed: 20550212 
• DOI: 10.1021/jm1000198
• Primary Citation of Related Structures:  
  3M11


• 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.

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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
Find proteins for O14965 (Homo sapiens) Explore O14965  Go to UniProtKB:  O14965
NIH Common Fund Data Resources
PHAROS:  O14965 GTEx:  ENSG00000087586

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKI	A	1-(4-{2-[(5,6-diphenylfuro[2,3-d]pyrimidin-4-yl)amino]ethyl}phenyl)-3-phenylurea C33 H27 N5 O2 SPKHBKVYERIGTO-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
AKI	IC50:  43   nM  BindingDB
AKI	IC50 :  43   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 82.266	α = 90
b = 82.266	β = 90
c = 170.283	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-03-03 
• Released Date: 2011-03-09 
Deposition Author(s): Wu, J.S., Leou, J.S., Coumar, M.S., Hsieh, H.P., Wu, S.Y.

Revision History  

• 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