Structural Basis for the Inhibition of Aurora A Kinase by a Novel Class of High Affinity Disubstituted Pyrimidine Inhibitors

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

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This is version 1.3 of the entry. See complete history


Structural basis for the inhibition of Aurora A kinase by a novel class of high affinity disubstituted pyrimidine inhibitors.

Tari, L.W.Hoffman, I.D.Bensen, D.C.Hunter, M.J.Nix, J.Nelson, K.J.McRee, D.E.Swanson, R.V.

(2007) Bioorg Med Chem Lett 17: 688-691

  • DOI: https://doi.org/10.1016/j.bmcl.2006.10.086
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The 2.25 A crystal structure of a complex of Aurora A kinase (AIKA) with cyclopropanecarboxylic acid-(3-(4-(3-trifluoromethyl-phenylamino)-pyrimidin-2-ylamino)-phenyl)-amide 1 is described here. The inhibitor binding mode is novel, with the cyclopropanecarboxylic acid moiety directed towards the solvent exposed region of the ATP-binding pocket, and several induced structural changes in the active-site compared with other published AIK structures. This structure provides context for the available SAR data on this compound class, and could be exploited for the design of analogs with increased affinity and selectivity for AIK.

  • Organizational Affiliation

    ActiveSight, 4045 Sorrento Valley Blvd., San Diego, CA 92121, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase 6272Homo sapiensMutation(s): 0 
Gene Names: AIK
UniProt & NIH Common Fund Data Resources
Find proteins for O14965 (Homo sapiens)
Explore O14965 
Go to UniProtKB:  O14965
PHAROS:  O14965
GTEx:  ENSG00000087586 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14965
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CC3

Download Ideal Coordinates CCD File 
C21 H18 F3 N5 O
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
CC3 Binding MOAD:  2NP8 IC50: 42 (nM) from 1 assay(s)
PDBBind:  2NP8 IC50: 42 (nM) from 1 assay(s)
BindingDB:  2NP8 IC50: 42 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.544α = 90
b = 81.544β = 90
c = 172.038γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description