Aurora A in complex with RPM1715

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.227 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


A Novel Mechanism by Which Small Molecule Inhibitors Induce the DFG Flip in Aurora A.

Martin, M.P.Zhu, J.Y.Lawrence, H.R.Pireddu, R.Luo, Y.Alam, R.Ozcan, S.Sebti, S.M.Lawrence, N.J.Schonbrunn, E.

(2012) ACS Chem Biol 7: 698-706

  • DOI: https://doi.org/10.1021/cb200508b
  • Primary Citation of Related Structures:  
    3UNJ, 3UNK, 3UNZ, 3UO4, 3UO5, 3UO6, 3UOD, 3UOH, 3UOJ, 3UOK, 3UOL, 3UP2

  • PubMed Abstract: 

    Most protein kinases share a DFG (Asp-Phe-Gly) motif in the ATP site that can assume two distinct conformations, the active DFG-in and the inactive DFG-out states. Small molecule inhibitors able to induce the DFG-out state have received considerable attention in kinase drug discovery. Using a typical DFG-in inhibitor scaffold of Aurora A, a kinase involved in the regulation of cell division, we found that halogen and nitrile substituents directed at the N-terminally flanking residue Ala273 induced global conformational changes in the enzyme, leading to DFG-out inhibitors that are among the most potent Aurora A inhibitors reported to date. The data suggest an unprecedented mechanism of action, in which induced-dipole forces along the Ala273 side chain alter the charge distribution of the DFG backbone, allowing the DFG to unwind. As the ADFG sequence and three-dimensional structure is highly conserved, DFG-out inhibitors of other kinases may be designed by specifically targeting the flanking alanine residue with electric dipoles.

  • Organizational Affiliation

    Drug Discovery Department, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase A
A, B
279Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for O14965 (Homo sapiens)
Explore O14965 
Go to UniProtKB:  O14965
PHAROS:  O14965
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14965
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0C5

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4-({4-[(2-cyanophenyl)amino]pyrimidin-2-yl}amino)benzoic acid
C18 H13 N5 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
0C5 PDBBind:  3UOJ Kd: 51 (nM) from 1 assay(s)
BindingDB:  3UOJ Kd: 51 (nM) from 1 assay(s)
IC50: 43 (nM) from 1 assay(s)
-TΔS: -2.59e+1 (kJ/mol) from 1 assay(s)
ΔH: -6.70e+1 (kJ/mol) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.227 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.71α = 90
b = 85.71β = 90
c = 77.08γ = 120
Software Package:
Software NamePurpose
StructureStudiodata collection
PHENIXmodel building
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2012-05-02
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description