3ZTX | pdb_00003ztx

Aurora kinase selective inhibitors identified using a Taxol-induced checkpoint sensitivity screen.

PDB DOI: https://doi.org/10.2210/pdb3ZTX/pdb

Classification: TRANSFERASE/CELL CYCLE
Organism(s): Xenopus laevis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-07-12 Released: 2012-02-01
Deposition Author(s): Kwiatkowski, N., Villa, F., Musacchio, A., Gray, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.226 (Depositor), 0.226 (DCC)
R-Value Work:
0.186 (Depositor), 0.185 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Selective Aurora Kinase Inhibitors Identified Using a Taxol- Induced Checkpoint Sensitivity Screen.

Kwiatkowski, N., Deng, X., Wang, J., Tan, L., Villa, F., Santaguida, S., Huang, H.C., Mitchison, T., Musacchio, A., Gray, N.

(2012) ACS Chem Biol 7: 185

PubMed: 21992004 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/cb200305u
Primary Citation Related Structures:
3ZTX

PubMed Abstract:
The members of the Aurora kinase family play critical roles in the regulation of the cell cycle and mitotic spindle assembly and have been intensively investigated as potential targets for a new class of anticancer drugs. We describe a new highly potent and selective class of Aurora kinase inhibitors discovered using a phenotypic cellular screen. Optimized inhibitors display many of the hallmarks of Aurora inhibition including endoreduplication, polyploidy, and loss of cell viability in cancer cells. Structure-activity relationships with respect to kinome-wide selectivity and guided by an Aurora B co-crystal structure resulted in the identification of key selectivity determinants and discovery of a subseries with selectivity toward Aurora A. A direct comparison of biochemical and cellular profiles with respect to published Aurora inhibitors including VX-680, AZD1152, MLN8054, and a pyrimidine-based compound from Genentech demonstrates that compounds 1 and 3 will become valuable additional pharmacological probes of Aurora-dependent functions.

Organizational Affiliation

Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, United States.

Macromolecule Content

Total Structure Weight: 78.08 kDa
Atom Count: 5,567
Modeled Residue Count: 626
Deposited Residue Count: 656
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE 12-A	A, B	284	Xenopus laevis	Mutation(s): 0 EC: 2.7.11.1
UniProt
Find proteins for Q6DE08 (Xenopus laevis) Explore Q6DE08 Go to UniProtKB: Q6DE08
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6DE08
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
INNER CENTROMERE PROTEIN A	C, D	44	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for O13024 (Xenopus laevis) Explore O13024 Go to UniProtKB: O13024
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O13024
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZTX Query on ZTX Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	2-((4-(4-HYDROXYPIPERIDIN-1-YL)PHENYL)AMINO)-5,11-DIMETHYL-5H-BENZO[E]PYRIMIDO [5,4-B][1,4]DIAZEPIN-6(11H)-ONE C₂₄ H₂₆ N₆ O₂ DFQAJLQXPSPNJE-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.226 (Depositor), 0.226 (DCC)
R-Value Work: 0.186 (Depositor), 0.185 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.634	α = 90
b = 66.364	β = 96.56
c = 116.679	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-02-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-01
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Other, Structure summary