3DAJ | pdb_00003daj

Crystal structure of Aurora A complexed with an inhibitor discovered through site-directed dynamic tethering

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.284 (Depositor) 
  • R-Value Work: 
    0.251 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 
    0.253 (Depositor) 

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This is version 1.3 of the entry. See complete history. 

Literature

Discovery of an Aurora kinase inhibitor through site-specific dynamic combinatorial chemistry.

Cancilla, M.T., He, M.M., Viswanathan, N., Simmons, R.L., Taylor, M., Fung, A.D., Cao, K., Erlanson, D.A.

(2008) Bioorg Med Chem Lett 18: 3978-3981

  • DOI: https://doi.org/10.1016/j.bmcl.2008.06.011
  • Primary Citation Related Structures: 
    3DAJ

  • PubMed Abstract: 

    We demonstrate a fragment-based lead discovery method that combines site-directed ligand discovery with dynamic combinatorial chemistry. Our technique targets dynamic combinatorial screening to a specified region of a protein by using reversible disulfide chemistry. We have used this technology to rapidly identify inhibitors of the drug target Aurora A that span the purine-binding site and the adaptive pocket of the kinase. The binding mode of a noncovalent inhibitor has been further characterized through crystallography.

    • Organizational Affiliation: 
    • Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, Suite 400, South San Francisco, CA 94080, USA.

Macromolecule Content 

  • Total Structure Weight: 31.99 kDa 
  • Atom Count: 2,132 
  • Modeled Residue Count: 245 
  • Deposited Residue Count: 272 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
serine/threonine kinase 6272Mus musculusMutation(s): 4 
Gene Names: Aurka, Stk6
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P97477 (Mus musculus)
Explore P97477 
Go to UniProtKB:  P97477
IMPC:  MGI:894678
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP97477
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FXG

Query on FXG


Download:Ideal Coordinates CCD File
B [auth A]N-butyl-3-{[6-(9H-purin-6-ylamino)hexanoyl]amino}benzamide
C22 H29 N7 O2
WOYITRCGMUXUDE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.284 (Depositor) 
  • R-Value Work:  0.251 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 0.253 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.932α = 90
b = 84.932β = 90
c = 77.025γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2008-07-08 
    • Deposition Author(s): He, M.M.

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-02-21
    Changes: Data collection