3MYG

Aurora A Kinase complexed with SCH 1473759

• PDB DOI: https://doi.org/10.2210/pdb3MYG/pdb

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


• Deposited: 2010-05-10 Released: 2010-07-21 
• Deposition Author(s): Hruza, A., Prosis, W., Ramanathan, L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.245 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 

Starting Model: experimental

Literature

Discovery of a Potent, Injectable Inhibitor of Aurora Kinases Based on the Imidazo-[1,2-a]-Pyrazine Core.

Yu, T., Tagat, J.R., Kerekes, A.D., Doll, R.J., Zhang, Y., Xiao, Y., Esposite, S., Belanger, D.B., Curran, P.J., Mandal, A.K., Siddiqui, M.A., Shih, N.Y., Basso, A.D., Liu, M., Gray, K., Tevar, S., Jones, J., Lee, S., Liang, L., Ponery, S., Smith, E.B., Hruza, A., Voigt, J., Ramanathan, L., Prosise, W., Hu, M.

(2010) ACS Med Chem Lett 1: 214-218

• PubMed: 24900197 
• DOI: https://doi.org/10.1021/ml100063w
• Primary Citation of Related Structures:  
  3MYG


• PubMed Abstract: 
  

  The imidazo-[1,2-a]-pyrazine (1) is a dual inhibitor of Aurora kinases A and B with modest cell potency (IC50 = 250 nM) and low solubility (5 μM). Lead optimization guided by the binding mode led to the acyclic amino alcohol 12k (SCH 1473759), which is a picomolar inhibitor of Aurora kinases (TdF K d Aur A = 0.02 nM and Aur B = 0.03 nM) with improved cell potency (phos-HH3 inhibition IC50 = 25 nM) and intrinsic aqueous solubility (11.4 mM). It also demonstrated efficacy and target engagement in human tumor xenograft mouse models.

---

Organizational Affiliation: 

Departments of Chemical Research.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 32.06 kDa 
• Atom Count: 2,171 
• Modelled Residue Count: 252 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase 6	A	272	Homo sapiens	Mutation(s): 0  Gene Names: AURKA, AIK, ARK1, AURA, BTAK, 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EML	C [auth A]	2-{ethyl[(5-{[6-methyl-3-(1H-pyrazol-4-yl)imidazo[1,2-a]pyrazin-8-yl]amino}isothiazol-3-yl)methyl]amino}-2-methylpropan-1-ol C20 H26 N8 O S RHGZQGXELRMGES-UHFFFAOYSA-N
PG4	B [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EML	PDBBind:  3MYG	Kd: 0.02 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.245 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.88	α = 90
b = 80.88	β = 90
c = 171.282	γ = 120

Software Package:

Software Name	Purpose
StructureStudio	data collection
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-21 
Deposition Author(s): Hruza, A., Prosis, W., Ramanathan, L.

Revision History  

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-04-18
  Changes: Data collection, Database references
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description