2NP8

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

• PDB DOI: https://doi.org/10.2210/pdb2NP8/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-10-26 Released: 2006-12-26 
• Deposition Author(s): Tari, L.W., Hoffman, I.D., Bensen, D.C., Hunter, M.J., Nix, J., Nelson, K.J., McRee, D.E., Swanson, R.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.283 
• R-Value Work: 0.244 
• R-Value Observed: 0.246 

Starting Model: experimental

Literature

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

• PubMed: 17157005 
• DOI: https://doi.org/10.1016/j.bmcl.2006.10.086
• Primary Citation of Related Structures:  
  2NP8


• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.05 kDa 
• Atom Count: 2,347 
• 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-protein kinase 6	A	272	Homo sapiens	Mutation(s): 0  Gene Names: AIK 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CC3	D [auth A]	N-{3-[(4-{[3-(TRIFLUOROMETHYL)PHENYL]AMINO}PYRIMIDIN-2-YL)AMINO]PHENYL}CYCLOPROPANECARBOXAMIDE C21 H18 F3 N5 O RDTDWGQDFJPTPD-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
CC3	PDBBind:  2NP8	IC50: 42 (nM) from 1 assay(s)
	BindingDB:  2NP8	IC50: 42 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 81.544	α = 90
b = 81.544	β = 90
c = 172.038	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-26 
Deposition Author(s): Tari, L.W., Hoffman, I.D., Bensen, D.C., Hunter, M.J., Nix, J., Nelson, K.J., McRee, D.E., Swanson, R.V.

Revision History  

• 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