6CPG

Structure of dephosphorylated Aurora A (122-403) in complex with inhibiting monobody and AT9283 in an inactive conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.285 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 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: https://doi.org/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. 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase AA,
C [auth D]
285Homo sapiensMutation(s): 0 
Gene Names: AURKAAIKAIRK1ARK1AURAAYK1BTAKIAK1STK15STK6
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14965
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MonobodyB,
D [auth E]
93synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
35R BindingDB:  6CPG IC50: 26 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.285 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.86α = 90
b = 69.7β = 90
c = 175.56γ = 90
Software Package:
Software NamePurpose
xia2data reduction
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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--
Department of Energy (DOE, United States)United 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: 2018-07-04
    Changes: Data collection, Source and taxonomy
  • Version 1.2: 2018-09-05
    Changes: Data collection, Source and taxonomy, Structure summary
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.5: 2022-03-16
    Changes: Author supporting evidence, Database references
  • Version 1.6: 2023-10-04
    Changes: Data collection, Refinement description