4DEA

Aurora A in complex with YL1-038-18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Development of o-Chlorophenyl Substituted Pyrimidines as Exceptionally Potent Aurora Kinase Inhibitors.

Lawrence, H.R.Martin, M.P.Luo, Y.Pireddu, R.Yang, H.Gevariya, H.Ozcan, S.Zhu, J.Y.Kendig, R.Rodriguez, M.Elias, R.Cheng, J.Q.Sebti, S.M.Schonbrunn, E.Lawrence, N.J.

(2012) J.Med.Chem. 55: 7392-7416

  • DOI: 10.1021/jm300334d
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The o-carboxylic acid substituted bisanilinopyrimidine 1 was identified as a potent hit (Aurora A IC(50) = 6.1 ± 1.0 nM) from in-house screening. Detailed structure-activity relationship (SAR) studies indicated that polar substituents at the para pos ...

    The o-carboxylic acid substituted bisanilinopyrimidine 1 was identified as a potent hit (Aurora A IC(50) = 6.1 ± 1.0 nM) from in-house screening. Detailed structure-activity relationship (SAR) studies indicated that polar substituents at the para position of the B-ring are critical for potent activity. X-ray crystallography studies revealed that compound 1 is a type I inhibitor that binds the Aurora kinase active site in a DFG-in conformation. Structure-activity guided replacement of the A-ring carboxylic acid with halogens and incorporation of fluorine at the pyrimidine 5-position led to highly potent inhibitors of Aurora A that bind in a DFG-out conformation. B-Ring modifications were undertaken to improve the solubility and cell permeability. Compounds such as 9m with water-solubilizing moieties at the para position of the B-ring inhibited the autophosphorylation of Aurora A in MDA-MB-468 breast cancer cells.


    Organizational Affiliation

    Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Molecular Oncology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Chemical Biology Core, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Molecular Medicine, University of South Florida, Tampa, FL 33620, USA.,Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aurora kinase A
A
279Homo sapiensMutation(s): 1 
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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NHI
Query on NHI

Download SDF File 
Download CCD File 
A
4,4'-(pyrimidine-2,4-diyldiimino)dibenzoic acid
C18 H14 N4 O4
PZRUXYWYONKHDD-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NHIIC50: 256 nM (99) BINDINGDB
NHIIC50: 256 nM BINDINGMOAD
NHIIC50: 256 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.218 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 82.420α = 90.00
b = 82.420β = 90.00
c = 174.100γ = 120.00
Software Package:
Software NamePurpose
StructureStudiodata collection
CNSrefinement
MOLREPphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2012-09-12
    Type: Database references
  • Version 1.2: 2012-09-26
    Type: Database references