8JMX | pdb_00008jmx

The crystal structure of human aurka kinase domain in complex with AURKA-A2

• PDB DOI: https://doi.org/10.2210/pdb8JMX/pdb

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


• Deposited: 2023-06-05 Released: 2023-10-18 
• Deposition Author(s): Zhu, C.J., Zhang, Z.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.306 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Multitarget inhibitors/probes that target LRRK2 and AURORA A kinases noncovalently and covalently.

Wang, W., Wang, X., Tang, G., Zhu, C., Xiang, M., Xiao, Q., Zhang, Z.M., Gao, L., Yao, S.Q.

(2023) Chem Commun (Camb) 59: 10789-10792

• PubMed: 37594149 
• DOI: https://doi.org/10.1039/d3cc03530a
• Primary Citation Related Structures: 
  8JMX


• PubMed Abstract: 
  

  Herein, we report a salicylaldehyde-based, reversible covalent inhibitor (A2) that possesses moderate cellular activity against AURKA with a prolonged residence time and shows significant non-covalent inhibition towards LRRK2. Our results indicated that this multitarget kinase inhibitor may be used as the starting point for future development of more potent, selective and dual-targeting covalent kinase inhibitors against AURKA and LRRK2 for mitophagy.

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Organizational Affiliation: 
• School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518000, China. [e-mail].
Department of Chemistry, National University of Singapore, Singapore 117543, Singapore. [e-mail].
School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.89 kDa 
• Atom Count: 1,956 
• Modeled Residue Count: 250 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aurora kinase A	A	263	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
E47 (Subject of Investigation/LOI)	B [auth A]	5-(4-morpholin-4-yl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)-2-oxidanyl-benzaldehyde C17 H16 N4 O3 OPQSSAIBYNXUAR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.306 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.133	α = 90
b = 83.133	β = 90
c = 171.452	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-18 
Deposition Author(s): Zhu, C.J., Zhang, Z.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-10-18
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary