Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.90 kDa 
• Atom Count: 2327 
• Modelled Residue Count: 266 
• Deposited Residue Count: 279 
• Unique protein chains: 1

4DEA

Aurora A in complex with YL1-038-18

• PDB DOI: 10.2210/pdb4DEA/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-01-20 Released: 2012-08-22 
• Deposition Author(s): Martin, M.P., Zhu, J.-Y., Schonbrunn, E.

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Experimental Data Snapshot

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

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

• PubMed: 22803810 
• DOI: 10.1021/jm300334d
• Primary Citation of Related Structures:  
  3UP7, 4DEA, 4DEB, 4DED, 4DEE


• 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 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.

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Organizational Affiliation: 

Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aurora kinase A	A	279	Homo sapiens	Mutation(s): 1  Gene Names: AIK, AIRK1, ARK1, AURA, AURKA, AYK1, BTAK, IAK1, STK15, STK6 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHI	E [auth A]	4,4'-(pyrimidine-2,4-diyldiimino)dibenzoic acid C18 H14 N4 O4 PZRUXYWYONKHDD-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NHI	PDBBind:  4DEA	IC50: 256 (nM) from 1 assay(s)
	BindingDB:  4DEA	IC50: 256 (nM) from 1 assay(s)
	Binding MOAD:  4DEA	IC50: 256 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.262 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.42	α = 90
b = 82.42	β = 90
c = 174.1	γ = 120

Software Package:

Software Name	Purpose
StructureStudio	data collection
MOLREP	phasing
CNS	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-20 
• Released Date: 2012-08-22 
Deposition Author(s): Martin, M.P., Zhu, J.-Y., Schonbrunn, E.

Revision History  

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