3EFW

Structure of AuroraA with pyridyl-pyrimidine urea inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Pyridyl-pyrimidine benzimidazole derivatives as potent, selective, and orally bioavailable inhibitors of Tie-2 kinase.

Cee, V.J.Cheng, A.C.Romero, K.Bellon, S.Mohr, C.Whittington, D.A.Bak, A.Bready, J.Caenepeel, S.Coxon, A.Deak, H.L.Fretland, J.Gu, Y.Hodous, B.L.Huang, X.Kim, J.L.Lin, J.Long, A.M.Nguyen, H.Olivieri, P.R.Patel, V.F.Wang, L.Zhou, Y.Hughes, P.Geuns-Meyer, S.

(2009) Bioorg Med Chem Lett 19: 424-427

  • DOI: 10.1016/j.bmcl.2008.11.056
  • Primary Citation of Related Structures:  
    3DA6, 3EFW, 3EWH

  • PubMed Abstract: 
  • Selective small molecule inhibitors of Tie-2 kinase are important tools for the validation of Tie-2 signaling in pathological angiogenesis. Reported herein is the optimization of a nonselective scaffold into a potent and highly selective inhibitor of Tie-2 kinase ...

    Selective small molecule inhibitors of Tie-2 kinase are important tools for the validation of Tie-2 signaling in pathological angiogenesis. Reported herein is the optimization of a nonselective scaffold into a potent and highly selective inhibitor of Tie-2 kinase.


    Organizational Affiliation

    Department of Medicinal Chemistry, Amgen Inc., One Kendall Square, Bldg. 1000, Cambridge, MA 02139, USA. vcee@amgen.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase 6A, B267Homo sapiensMutation(s): 0 
Gene Names: AURKAAIKARK1AURABTAKSTK15STK6AIRK1AYK1IAK1
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
GTEx:  ENSG00000087586 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14965
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AK8
Query on AK8

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
1-[3-methyl-4-({3-[2-(methylamino)pyrimidin-4-yl]pyridin-2-yl}oxy)phenyl]-3-[3-(trifluoromethyl)phenyl]urea
C25 H21 F3 N6 O2
INFGJUQNPPGDNS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
AK8 PDBBind:  3EFW IC50: 4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.511α = 90
b = 125.448β = 90
c = 75.752γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata 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: 2008-12-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Database references, Structure summary
  • Version 1.3: 2013-06-26
    Changes: Database references