5OBJ | pdb_00005obj

Aurora A kinase in complex with 2-(3-fluorophenyl)quinoline-4-carboxylic acid and ATP

• PDB DOI: https://doi.org/10.2210/pdb5OBJ/pdb

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


• Deposited: 2017-06-28 Released: 2017-08-09 
• Deposition Author(s): Rossmann, M., Janecek, M., Hyvonen, M.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Literature

Computationally-guided optimization of small-molecule inhibitors of the Aurora A kinase-TPX2 protein-protein interaction.

Cole, D.J., Janecek, M., Stokes, J.E., Rossmann, M., Faver, J.C., McKenzie, G.J., Venkitaraman, A.R., Hyvonen, M., Spring, D.R., Huggins, D.J., Jorgensen, W.L.

(2017) Chem Commun (Camb) 53: 9372-9375

• PubMed: 28787041 
• DOI: https://doi.org/10.1039/c7cc05379g
• Primary Citation Related Structures: 
  5OBJ, 5OBR


• PubMed Abstract: 
  

  Free energy perturbation theory, in combination with enhanced sampling of protein-ligand binding modes, is evaluated in the context of fragment-based drug design, and used to design two new small-molecule inhibitors of the Aurora A kinase-TPX2 protein-protein interaction.

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Organizational Affiliation: 
• Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA and School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, UK. [e-mail].
MRC Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Old Addenbrooke's Site, Cambridge CB2 1GA, UK.
Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA.
MRC Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK.
MRC Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK and Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, Cambridge CB3 0HE, UK.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.38 kDa 
• Atom Count: 2,186 
• Modeled Residue Count: 260 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aurora kinase A	A	272	Homo sapiens	Mutation(s): 0  Gene Names: AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	E [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
9QK	F [auth A]	2-(3-fluorophenyl)quinoline-4-carboxylic acid C16 H10 F N O2 PCKQJQMHOYYDMQ-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.41	α = 90
b = 83.41	β = 90
c = 172.09	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Rossmann, M., Janecek, M., Hyvonen, M.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	090340/Z/09/Z

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references