Aurora A in complex with YL1-038-09

Experimental Data Snapshot

  • Resolution: 3.05 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


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: https://doi.org/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.

  • Organizational Affiliation

    Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase A279Homo 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 0C9

Download Ideal Coordinates CCD File 
B [auth A]2-({2-[(4-carboxyphenyl)amino]pyrimidin-4-yl}amino)benzoic acid
C18 H14 N4 O4
Binding Affinity Annotations 
IDSourceBinding Affinity
0C9 BindingDB:  3UP7 Kd: 34 (nM) from 1 assay(s)
IC50: 6.1 (nM) from 1 assay(s)
-TΔS: -1.40e+1 (kJ/mol) from 1 assay(s)
ΔH: -5.90e+1 (kJ/mol) from 1 assay(s)
PDBBind:  3UP7 IC50: 6.1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.05 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.58α = 90
b = 82.58β = 90
c = 172.36γ = 120
Software Package:
Software NamePurpose
StructureStudiodata collection
PHENIXmodel building
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

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: 2012-08-22
    Changes: Database references
  • Version 1.3: 2012-09-26
    Changes: Database references
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description