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- PDB-3ztx: Aurora kinase selective inhibitors identified using a Taxol-induc... -

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Basic information

Entry
Database: PDB / ID: 3ztx
TitleAurora kinase selective inhibitors identified using a Taxol-induced checkpoint sensitivity screen.
Components
  • INNER CENTROMERE PROTEIN A
  • SERINE/THREONINE-PROTEIN KINASE 12-A
KeywordsTRANSFERASE/CELL CYCLE / TRANSFERASE-CELL CYCLE COMPLEX / TRANSFERASE / TAXOL-INDUCED CHECKPOINT INHIBITOR
Function / homology
Function and homology information


mitotic cytokinesis checkpoint signaling / negative regulation of cytokinesis / positive regulation of mitotic sister chromatid segregation / abscission / mitotic spindle midzone assembly / cleavage furrow formation / histone H3S10 kinase activity / chromosome passenger complex / protein localization to kinetochore / negative regulation of B cell apoptotic process ...mitotic cytokinesis checkpoint signaling / negative regulation of cytokinesis / positive regulation of mitotic sister chromatid segregation / abscission / mitotic spindle midzone assembly / cleavage furrow formation / histone H3S10 kinase activity / chromosome passenger complex / protein localization to kinetochore / negative regulation of B cell apoptotic process / positive regulation of cytokinesis / mitotic cytokinesis / chromosome, centromeric region / spindle assembly / pericentric heterochromatin / post-translational protein modification / chromosome segregation / kinetochore / spindle / cellular response to UV / chromosome / midbody / microtubule / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / chromatin / protein kinase binding / negative regulation of transcription by RNA polymerase II / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2990 / Inner centromere protein, ARK-binding domain / Chromosome passenger complex (CPC) protein INCENP N-terminal / Inner centromere protein, ARK binding region / Chromosome passenger complex (CPC) protein INCENP N terminal / Aurora kinase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Transferase(Phosphotransferase) domain 1 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2990 / Inner centromere protein, ARK-binding domain / Chromosome passenger complex (CPC) protein INCENP N-terminal / Inner centromere protein, ARK binding region / Chromosome passenger complex (CPC) protein INCENP N terminal / Aurora kinase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-ZTX / Inner centromere protein A / Aurora kinase B-A
Similarity search - Component
Biological speciesXENOPUS LAEVIS (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKwiatkowski, N. / Villa, F. / Musacchio, A. / Gray, N.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: Selective Aurora Kinase Inhibitors Identified Using a Taxol- Induced Checkpoint Sensitivity Screen.
Authors: Kwiatkowski, N. / Deng, X. / Wang, J. / Tan, L. / Villa, F. / Santaguida, S. / Huang, H.C. / Mitchison, T. / Musacchio, A. / Gray, N.
History
DepositionJul 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE 12-A
B: SERINE/THREONINE-PROTEIN KINASE 12-A
C: INNER CENTROMERE PROTEIN A
D: INNER CENTROMERE PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0846
Polymers77,2234
Non-polymers8612
Water5,134285
1
A: SERINE/THREONINE-PROTEIN KINASE 12-A
D: INNER CENTROMERE PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0423
Polymers38,6122
Non-polymers4311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-24.4 kcal/mol
Surface area15570 Å2
MethodPISA
2
B: SERINE/THREONINE-PROTEIN KINASE 12-A
C: INNER CENTROMERE PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0423
Polymers38,6122
Non-polymers4311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-23.2 kcal/mol
Surface area15900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.634, 66.364, 116.679
Angle α, β, γ (deg.)90.00, 96.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE 12-A / AURORA B / AURORA KINASE B-A / AURORA/IPL1-RELATED KINASE 2 / A XAIRK2 / SERINE/THREONINE-PROTEIN ...AURORA B / AURORA KINASE B-A / AURORA/IPL1-RELATED KINASE 2 / A XAIRK2 / SERINE/THREONINE-PROTEIN KINASE AURORA-B-A / XAURORA-B


Mass: 33537.871 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 78-361
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q6DE08, non-specific serine/threonine protein kinase
#2: Protein/peptide INNER CENTROMERE PROTEIN A / XL-INCENP / XINC / XINCENP / MITOTIC PHOSPHOPROTEIN 130


Mass: 5073.755 Da / Num. of mol.: 2 / Fragment: RESIDUES 797-840
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O13024
#3: Chemical ChemComp-ZTX / 2-((4-(4-HYDROXYPIPERIDIN-1-YL)PHENYL)AMINO)-5,11-DIMETHYL-5H-BENZO[E]PYRIMIDO [5,4-B][1,4]DIAZEPIN-6(11H)-ONE


Mass: 430.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H26N6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.85→35 Å / Num. obs: 60077 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.3
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.9 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→34.68 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.507 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22597 2561 5.1 %RANDOM
Rwork0.18569 ---
obs0.18775 47899 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.07 Å2
2--0.18 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.95→34.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 64 285 5545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225433
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.641.9897342
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9965629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92422.765264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41715980
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3181549
X-RAY DIFFRACTIONr_chiral_restr0.110.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214166
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9911.53149
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.79225104
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.78932284
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6364.52235
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 158 -
Rwork0.222 3544 -
obs--99.22 %

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