9BZL | pdb_00009bzl

Targeting N-Myc in Neuroblastoma with Selective Aurora Kinase A Degraders

• PDB DOI: https://doi.org/10.2210/pdb9BZL/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-05-24 Released: 2025-01-15 
• Deposition Author(s): Baker, Z.D., Tang, J., Shi, K., Aihara, H., Levinson, N.M., Harki, D.A.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), Department of Defense (DOD, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.214 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Targeting N-Myc in neuroblastoma with selective Aurora kinase A degraders.

Tang, J., Moorthy, R., Hirsch, L.E., Demir, O., Baker, Z.D., Naumann, J.A., Jones, K.F.M., Grillo, M.J., Haefner, E.S., Shi, K., Levy, M.J., Gupta, H.B., Aihara, H., Harris, R.S., Amaro, R.E., Levinson, N.M., Harki, D.A.

(2025) Cell Chem Biol 32: 352

• PubMed: 39778578 
• DOI: https://doi.org/10.1016/j.chembiol.2024.12.006
• Primary Citation of Related Structures:  
  9BZG, 9BZL


• PubMed Abstract: 
  

  The N-Myc transcription factor, encoded by MYCN, is a mechanistically validated, yet challenging, target for neuroblastoma (NB) therapy development. In normal neuronal progenitors, N-Myc undergoes rapid degradation, while, in MYCN-amplified NB cells, Aurora kinase A (Aurora-A) binds to and stabilizes N-Myc, resulting in elevated protein levels. Here, we demonstrate that targeted protein degradation of Aurora-A decreases N-Myc levels. A potent Aurora-A degrader, HLB-0532259 (compound 4), was developed from an Aurora-A-binding ligand that engages the Aurora-A/N-Myc complex. HLB-0532259 promotes the degradation of Aurora-A, which elicits concomitant N-Myc degradation, with nanomolar potency and excellent selectivity. HLB-0532259 surpasses the cellular efficacy of established allosteric Aurora-A inhibitors, exhibits favorable pharmacokinetic properties, and elicits tumor reduction in a murine xenograft NB model. This study broadly delineates a strategy for targeting "undruggable" proteins that are reliant on accessory proteins for cellular stabilization.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA.
Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
KCAS Bioanalytical and Biomarker Services, Olathe, KS 66061, USA.
Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA.
Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA.
Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA. Electronic address: [e-mail].

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: 33.39 kDa 
• Atom Count: 2,277 
• Modeled Residue Count: 262 
• Deposited Residue Count: 285 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aurora kinase A	A [auth B]	285	Homo sapiens	Mutation(s): 2  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
OGR (Subject of Investigation/LOI)	B	7-cyclopentyl-N,N-dimethyl-2-{[5-(methylcarbamoyl)pyridin-2-yl]amino}-7H-pyrrolo[2,3-d]pyrimidine-6-carboxamide C21 H25 N7 O2 ZWAGHYMVHPAUMT-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A [auth B]	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.214 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.752	α = 90
b = 83.752	β = 90
c = 77.54	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
Coot	model building
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Baker, Z.D., Tang, J., Shi, K., Aihara, H., Levinson, N.M., Harki, D.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P01-CA234228
Department of Defense (DOD, United States)	United States	W81XWH-21-1-0674

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release
  
• Version 1.1: 2025-01-22
  Changes: Database references
• Version 1.2: 2025-03-05
  Changes: Database references