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: 2.8 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.279 

wwPDB Validation 3D Report Full Report


This is version 1.4 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:  

  • 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 h ...

    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.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aurora kinase A
A, D
285Homo sapiensMutation(s): 0 
Gene Names: AURKA (AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6)
EC: 2.7.11.1
Find proteins for O14965 (Homo sapiens)
Go to Gene View: AURKA
Go to UniProtKB:  O14965
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Monobody
B, E
93N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
35R
Query on 35R

Download SDF File 
Download CCD File 
A, D
1-cyclopropyl-3-{3-[5-(morpholin-4-ylmethyl)-1H-benzimidazol-2-yl]-1H-pyrazol-4-yl}urea
C19 H23 N7 O2
LOLPPWBBNUVNQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.279 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.860α = 90.00
b = 69.700β = 90.00
c = 175.560γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
xia2data reduction
XDSdata scaling
PHENIXrefinement
XDSdata reduction
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-07-04
    Type: Data collection, Source and taxonomy
  • Version 1.2: 2018-09-05
    Type: Data collection, Source and taxonomy, Structure summary
  • Version 1.3: 2019-02-20
    Type: Author supporting evidence, Data collection
  • Version 1.4: 2019-11-20
    Type: Author supporting evidence