3P9J

Aurora A kinase domain with phthalazinone pyrazole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3P9J/pdb

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


• Deposited: 2010-10-17 Released: 2011-03-23 
• Deposition Author(s): Kairies, N.A., Oliveira, T., Engh, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.271 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 

Literature

Phthalazinone pyrazoles as potent, selective, and orally bioavailable inhibitors of aurora-a kinase.

Prime, M.E., Courtney, S.M., Brookfield, F.A., Marston, R.W., Walker, V., Warne, J., Boyd, A.E., Kairies, N.A., von der Saal, W., Limberg, A., Georges, G., Engh, R.A., Goller, B., Rueger, P., Rueth, M.

(2011) J Med Chem 54: 312-319

• PubMed: 21128645 
• DOI: https://doi.org/10.1021/jm101346r
• Primary Citation of Related Structures:  
  3P9J


• PubMed Abstract: 
  

  The inhibition of Aurora kinases in order to arrest mitosis and subsequently inhibit tumor growth via apoptosis of proliferating cells has generated significant discussion within the literature. We report a novel class of Aurora kinase inhibitors based upon a phthalazinone pyrazole scaffold. The development of the phthalazinone template resulted in a potent Aurora-A selective series of compounds (typically >1000-fold selectivity over Aurora-B) that display good pharmacological profiles with significantly improved oral bioavailability compared to the well studied Aurora inhibitor VX-680.

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Organizational Affiliation: 

Evotec (UK) Ltd., 114 Milton Park, Abingdon, UK. [e-mail]

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: 31.37 kDa 
• Atom Count: 2,084 
• Modelled Residue Count: 249 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase 6	A	268	Homo sapiens	Mutation(s): 2  Gene Names: AIK, ARK1, AURA, AURKA, BTAK, 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
P9J	B [auth A]	4-[(5-methyl-1H-pyrazol-3-yl)amino]-2-phenylphthalazin-1(2H)-one C18 H15 N5 O DSDIWWSXOOXFSI-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
P9J	PDBBind:  3P9J	IC50: 31 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.271 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.113	α = 90
b = 83.113	β = 90
c = 169.191	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-23 
Deposition Author(s): Kairies, N.A., Oliveira, T., Engh, R.A.

Revision History  

• Version 1.0: 2011-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-10-05
  Changes: Database references
• Version 1.3: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Derived calculations