3D15 | pdb_00003d15

Crystal structure of mouse Aurora A (Asn186->Gly, Lys240->Arg, Met302->Leu) in complex with 1-(3-chloro-phenyl)-3-{5-[2-(thieno[3,2-d]pyrimidin-4-ylamino)- ethyl]-thiazol-2-yl}-urea [SNS-314]

• PDB DOI: https://doi.org/10.2210/pdb3D15/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-05-04 Released: 2009-05-12 
• Deposition Author(s): Elling, R.A., Bui, M., Allen, D.A., Oslob, J.D., Romanowski, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.287 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

Discovery of a potent and selective aurora kinase inhibitor.

Oslob, J.D., Romanowski, M.J., Allen, D.A., Baskaran, S., Bui, M., Elling, R.A., Flanagan, W.M., Fung, A.D., Hanan, E.J., Harris, S., Heumann, S.A., Hoch, U., Jacobs, J.W., Lam, J., Lawrence, C.E., McDowell, R.S., Nannini, M.A., Shen, W., Silverman, J.A., Sopko, M.M., Tangonan, B.T., Teague, J., Yoburn, J.C., Yu, C.H., Zhong, M., Zimmerman, K.M., O'Brien, T., Lew, W.

(2008) Bioorg Med Chem Lett 18: 4880-4884

• PubMed: 18678489 
• DOI: https://doi.org/10.1016/j.bmcl.2008.07.073
• Primary Citation of Related Structures:  
  3D14, 3D15


• PubMed Abstract: 
  

  This communication describes the discovery of a novel series of Aurora kinase inhibitors. Key SAR and critical binding elements are discussed. Some of the more advanced analogues potently inhibit cellular proliferation and induce phenotypes consistent with Aurora kinase inhibition. In particular, compound 21 (SNS-314) is a potent and selective Aurora kinase inhibitor that exhibits significant activity in pre-clinical in vivo tumor models.

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Organizational Affiliation: 

Medicinal Chemistry, Sunesis Pharmaceuticals, 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 31.98 kDa 
• Atom Count: 2,238 
• Modelled Residue Count: 256 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
serine/threonine kinase 6	A	272	Mus musculus	Mutation(s): 3  Gene Names: Aurka, Stk6 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P97477 (Mus musculus) Explore P97477  Go to UniProtKB:  P97477
IMPC:  MGI:894678

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AK2	B [auth A]	1-(3-chlorophenyl)-3-{5-[2-(thieno[3,2-d]pyrimidin-4-ylamino)ethyl]-1,3-thiazol-2-yl}urea C18 H15 Cl N6 O S2 FAYAUAZLLLJJGH-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AK2	BindingDB:  3D15	IC50: min: 9, max: 9 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.287 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.353	α = 90
b = 82.353	β = 90
c = 171.999	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
CrystalClear	data reduction
d*TREK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-12 
Deposition Author(s): Elling, R.A., Bui, M., Allen, D.A., Oslob, J.D., Romanowski, M.J.

Revision History  

• Version 1.0: 2009-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-06-19
  Changes: Database references
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description