3UNJ

CDK2 in complex with inhibitor YL1-038-31


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9001 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1021/cb200508b
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 2
A
298Homo sapiensMutation(s): 0 
Gene Names: CDK2 (CDKN2)
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Go to Gene View: CDK2
Go to UniProtKB:  P24941
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
0BX
Query on 0BX

Download SDF File 
Download CCD File 
A
4-{[4-(phenylamino)pyrimidin-2-yl]amino}benzoic acid
C17 H14 N4 O2
BUKMSYYNNHEANR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0BXIC50: 11000 nM BINDINGMOAD
0BXIC50: 11000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9001 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.220α = 90.00
b = 71.960β = 90.00
c = 72.650γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXmodel building
PHENIXrefinement
PHENIXphasing
StructureStudiodata collection
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2012-05-02
    Type: Database references