2J50 | pdb_00002j50

Structure of Aurora-2 in complex with PHA-739358

• PDB DOI: https://doi.org/10.2210/pdb2J50/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2006-09-08 Released: 2006-11-06 
• Deposition Author(s): Cameron, A.D., Izzo, G., Storici, P., Rusconi, L., Fancelli, D., Varasi, M., Berta, D., Bindi, S., Forte, B., Severino, D., Tonani, R., Vianello, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.268 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 

Starting Model: experimental

Literature

1,4,5,6-Tetrahydropyrrolo[3,4-C]Pyrazoles: Identification of a Potent Aurora Kinase Inhibitor with a Favorable Antitumor Kinase Inhibition Profile.

Fancelli, D., Moll, J., Varasi, M., Bravo, R., Artico, R., Berta, D., Bindi, S., Cameron, A.D., Candiani, I., Cappella, P., Carpinelli, P., Croci, W., Forte, B., Giorgini, M.L., Klapwijk, J., Marsiglio, A., Pesenti, E., Rocchetti, M., Roletto, F., Severino, D., Soncini, C., Storici, P., Tonani, R., Zugnoni, P., Vianello, P.

(2006) J Med Chem 49: 7247

• PubMed: 17125279 
• DOI: https://doi.org/10.1021/jm060897w
• Primary Citation Related Structures: 
  2J4Z, 2J50


• PubMed Abstract: 
  

  The optimization of a series of 5-phenylacetyl 1,4,5,6-tetrahydropyrrolo[3,4-c]pyrazole derivatives toward the inhibition of Aurora kinases led to the identification of compound 9d. This is a potent inhibitor of Aurora kinases that also shows low nanomolar potency against additional anticancer kinase targets. Based on its high antiproliferative activity on different cancer cell lines, favorable chemico-physical and pharmacokinetic properties, and high efficacy in in vivo tumor models, compound 9d was ultimately selected for further development.

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Organizational Affiliation: 
• Nerviano Medical Sciences S.r.l. viale Pasteur 10, 20014 Nerviano, Milan, Italy.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 65.88 kDa 
• Atom Count: 4,164 
• Modeled Residue Count: 500 
• Deposited Residue Count: 560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE 6	A, B	280	Homo sapiens	Mutation(s): 0  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
627	C [auth A], E [auth B]	N-[(3E)-5-[(2R)-2-METHOXY-2-PHENYLACETYL]PYRROLO[3,4-C]PYRAZOL-3(5H)-YLIDENE]-4-(4-METHYLPIPERAZIN-1-YL)BENZAMIDE C26 H30 N6 O3 XKFTZKGMDDZMJI-HSZRJFAPSA-N
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
627	BindingDB:  2J50	IC50: 13 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.268 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.688	α = 90
b = 86.782	β = 90
c = 86.829	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-06 
Deposition Author(s): Cameron, A.D., Izzo, G., Storici, P., Rusconi, L., Fancelli, D., Varasi, M., Berta, D., Bindi, S., Forte, B., Severino, D., Tonani, R., Vianello, P.

Revision History  

• Version 1.0: 2006-11-06
  Type: Initial release
  
• Version 1.1: 2015-07-29
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2019-04-03
  Changes: Data collection, Other, Source and taxonomy
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2026-03-04
  Changes: Refinement description, Structure summary