Biological Assembly 1  

 3D View: Structure | 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: 32.34 kDa 
• Atom Count: 2075 
• Modelled Residue Count: 252 
• Deposited Residue Count: 275 
• Unique protein chains: 1

2W1D

Structure determination of Aurora Kinase in complex with inhibitor

• DOI: 10.2210/pdb2W1D/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-10-17 Released: 2009-01-27 
• Deposition Author(s): Howard, S., Berdini, V., Boulstridge, J.A., Carr, M.G., Cross, D.M., Curry, J., Devine, L.A., Early, T.R., Fazal, L., Gill, A.L., Heathcote, M., Maman, S., Matthews, J.E., McMenamin, R.L., Navarro, E.F., O'Brien, M.A., O'Reilly, M., Rees, D.C., Reule, M., Tisi, D., Williams, G., Vinkovic, M., Wyatt, P.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.97 Å
• R-Value Free: 0.308 
• R-Value Work: 0.236 
• R-Value Observed: 0.241 

Literature

Fragment-Based Discovery of the Pyrazol-4-Yl Urea (at9283), a Multitargeted Kinase Inhibitor with Potent Aurora Kinase Activity.

Howard, S., Berdini, V., Boulstridge, J.A., Carr, M.G., Cross, D.M., Curry, J., Devine, L.A., Early, T.R., Fazal, L., Gill, A.L., Heathcote, M., Maman, S., Matthews, J.E., Mcmenamin, R.L., Navarro, E.F., O'Brien, M.A., O'Reilly, M., Rees, D.C., Reule, M., Tisi, D., Williams, G., Vinkovic, M., Wyatt, P.G.

(2009) J Med Chem 52: 379

• PubMed: 19143567 
• DOI: 10.1021/jm800984v
• Primary Citation of Related Structures:  
  2W1C, 2W1D, 2W1E, 2W1F, 2W1G, 2W1H, 2W1I


• PubMed Abstract: 
  

Here, we describe the identification of a clinical candidate via structure-based optimization of a ligand efficient pyrazole-benzimidazole fragment. Aurora kinases play a key role in the regulation of mitosis and in recent years have become attractive targets for the treatment of cancer. X-ray crystallographic structures were generated using a novel soakable form of Aurora A and were used to drive the optimization toward potent (IC(50) approximately 3 nM) dual Aurora A/Aurora B inhibitors. These compounds inhibited growth and survival of HCT116 cells and produced the polyploid cellular phenotype typically associated with Aurora B kinase inhibition. Optimization of cellular activity and physicochemical properties ultimately led to the identification of compound 16 (AT9283). In addition to Aurora A and Aurora B, compound 16 was also found to inhibit a number of other kinases including JAK2 and Abl (T315I). This compound demonstrated in vivo efficacy in mouse xenograft models and is currently under evaluation in phase I clinical trials.

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Organizational Affiliation: 

Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE 6	A	275	Homo sapiens	Mutation(s): 0  Gene Names: AURKA, AIK, AIRK1, ARK1, AURA, 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 GTEx:  ENSG00000087586

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L0D (Subject of Investigation/LOI)	B [auth A]	2-(1H-pyrazol-3-yl)-1H-benzimidazole C10 H8 N4 IYTGPPNUOLLGBE-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
L0D	BindingDB:  2W1D	IC50: 910 (nM) from 1 assay(s)
	PDBBind:  2W1D	IC50: 910 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.97 Å
• R-Value Free: 0.308 
• R-Value Work: 0.236 
• R-Value Observed: 0.241 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.008	α = 90
b = 83.008	β = 90
c = 169.719	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2008-10-17 
• Released Date: 2009-01-27 
Deposition Author(s): Howard, S., Berdini, V., Boulstridge, J.A., Carr, M.G., Cross, D.M., Curry, J., Devine, L.A., Early, T.R., Fazal, L., Gill, A.L., Heathcote, M., Maman, S., Matthews, J.E., McMenamin, R.L., Navarro, E.F., O'Brien, M.A., O'Reilly, M., Rees, D.C., Reule, M., Tisi, D., Williams, G., Vinkovic, M., Wyatt, P.G.

Revision History  

• Version 1.0: 2009-01-27
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance