6CPF

Structure of dephosphorylated Aurora A (122-403) bound to AMPPCP in an active conformation

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

  • Deposited: 2018-03-13 Released: 2018-06-27 
  • Deposition Author(s): Otten, R., Zorba, A., Padua, R.A.P., Kern, D.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI), Office of Basic Energy Sciences, Catalysis Science Program, U.S. Dept. of Energy, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Dynamics of human protein kinase Aurora A linked to drug selectivity.

Pitsawong, W., Buosi, V., Otten, R., Agafonov, R.V., Zorba, A., Kern, N., Kutter, S., Kern, G., Padua, R.A., Meniche, X., Kern, D.

(2018) Elife 7

  • DOI: 10.7554/eLife.36656
  • Primary Citation of Related Structures:  
    6CPE, 6CPF, 6CPG

  • PubMed Abstract: 

    • Protein kinases are major drug targets, but the development of highly-selective inhibitors has been challenging due to the similarity of their active sites. The observation of distinct structural states of the fully-conserved Asp-Phe-Gly (DFG) loop has put the concept of conformational selection for the DFG-state at the center of kinase drug discovery ...

    Protein kinases are major drug targets, but the development of highly-selective inhibitors has been challenging due to the similarity of their active sites. The observation of distinct structural states of the fully-conserved Asp-Phe-Gly (DFG) loop has put the concept of conformational selection for the DFG-state at the center of kinase drug discovery. Recently, it was shown that Gleevec selectivity for the Tyr-kinase Abl was instead rooted in conformational changes after drug binding. Here, we investigate whether protein dynamics after binding is a more general paradigm for drug selectivity by characterizing the binding of several approved drugs to the Ser/Thr-kinase Aurora A. Using a combination of biophysical techniques, we propose a universal drug-binding mechanism, that rationalizes selectivity, affinity and long on-target residence time for kinase inhibitors. These new concepts, where protein dynamics in the drug-bound state plays the crucial role, can be applied to inhibitor design of targets outside the kinome.

    Organizational Affiliation: 

    Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aurora kinase AA285Homo sapiensMutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACP (Subject of Investigation/LOI)
Query on ACP
Download Ideal Coordinates CCD File 
B [auth A]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.222 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.75α = 90
b = 81.75β = 90
c = 172.871γ = 120
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment  


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
Office of Basic Energy Sciences, Catalysis Science ProgramUnited States--
U.S. Dept. of EnergyUnited StatesDE-FG02-05ER15699
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM100966-01

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence