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- PDB-3myg: Aurora A Kinase complexed with SCH 1473759 -

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Basic information

Entry
Database: PDB / ID: 3myg
TitleAurora A Kinase complexed with SCH 1473759
ComponentsSerine/threonine-protein kinase 6Serine/threonine-specific protein kinase
KeywordsTRANSFERASE / Kinase / Cell Cycle / Inhibitor
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / meiotic spindle / mitotic centrosome separation / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / positive regulation of mitochondrial fission / spindle organization / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic cell cycle / AURKA Activation by TPX2 / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of mitotic nuclear division / ciliary basal body / negative regulation of protein binding / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / molecular function activator activity / liver regeneration / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / regulation of protein stability / mitotic spindle / spindle / kinetochore / response to wounding / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / microtubule / postsynaptic density / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / cell division / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Aurora kinase A / Aurora kinase / 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 ...Aurora kinase A / Aurora kinase / 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-EML / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsHruza, A. / Prosis, W. / Ramanathan, L.
CitationJournal: ACS Med Chem Lett / Year: 2010
Title: Discovery of a Potent, Injectable Inhibitor of Aurora Kinases Based on the Imidazo-[1,2-a]-Pyrazine Core.
Authors: Yu, T. / Tagat, J.R. / Kerekes, A.D. / Doll, R.J. / Zhang, Y. / Xiao, Y. / Esposite, S. / Belanger, D.B. / Curran, P.J. / Mandal, A.K. / Siddiqui, M.A. / Shih, N.Y. / Basso, A.D. / Liu, M. / ...Authors: Yu, T. / Tagat, J.R. / Kerekes, A.D. / Doll, R.J. / Zhang, Y. / Xiao, Y. / Esposite, S. / Belanger, D.B. / Curran, P.J. / Mandal, A.K. / Siddiqui, M.A. / Shih, N.Y. / Basso, A.D. / Liu, M. / Gray, K. / Tevar, S. / Jones, J. / Lee, S. / Liang, L. / Ponery, S. / Smith, E.B. / Hruza, A. / Voigt, J. / Ramanathan, L. / Prosise, W. / Hu, M.
History
DepositionMay 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Serine/threonine-protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0613
Polymers31,4401
Non-polymers6212
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.880, 80.880, 171.282
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Serine/threonine-protein kinase 6 / Serine/threonine-specific protein kinase / Aurora kinase A / Serine/threonine-protein kinase aurora-A / Serine/threonine-protein kinase 15 / ...Aurora kinase A / Serine/threonine-protein kinase aurora-A / Serine/threonine-protein kinase 15 / Aurora/IPL1-related kinase 1 / Aurora-related kinase 1 / ARK-1 / hARK1 / Breast tumor-amplified kinase


Mass: 31440.150 Da / Num. of mol.: 1 / Fragment: UNP Residues 126-391
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AURKA, AIK, ARK1, AURA, BTAK, STK15, STK6 / Plasmid: pDest14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-EML / 2-{ethyl[(5-{[6-methyl-3-(1H-pyrazol-4-yl)imidazo[1,2-a]pyrazin-8-yl]amino}isothiazol-3-yl)methyl]amino}-2-methylpropan-1-ol / SCH 1473759


Mass: 426.538 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N8OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.1M Tris, 0.2M LiSO4, 33% PEG 400, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 27, 2007 / Details: OSMIC
RadiationMonochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→35 Å / Num. all: 13858 / Num. obs: 13705 / Observed criterion σ(I): 2.3 / Redundancy: 4.2 % / Biso Wilson estimate: 63.39 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1210 / % possible all: 91.3

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Processing

Software
NameVersionClassification
StructureStudiodata collection
BUSTER2.9.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1MQ4

1mq4


Resolution: 2.4→32.42 Å / Cor.coef. Fo:Fc: 0.9291 / Cor.coef. Fo:Fc free: 0.9189 / SU R Cruickshank DPI: 0.235 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.375 / SU Rfree Blow DPI: 0.237 / SU Rfree Cruickshank DPI: 0.352 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 714 5.25 %RANDOM
Rwork0.2211 ---
obs0.2224 13611 98.62 %-
Displacement parametersBiso mean: 58.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.4277 Å20 Å20 Å2
2--4.4277 Å20 Å2
3----8.8554 Å2
Refine analyzeLuzzati coordinate error obs: 0.343 Å
Refinement stepCycle: LAST / Resolution: 2.4→32.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2081 0 43 47 2171
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00921782
X-RAY DIFFRACTIONt_angle_deg1.0929292
X-RAY DIFFRACTIONt_dihedral_angle_d7562
X-RAY DIFFRACTIONt_trig_c_planes492
X-RAY DIFFRACTIONt_gen_planes3115
X-RAY DIFFRACTIONt_it217820
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion20.19
X-RAY DIFFRACTIONt_chiral_improper_torsion2615
X-RAY DIFFRACTIONt_ideal_dist_contact24714
LS refinement shellResolution: 2.4→2.58 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3306 144 5.58 %
Rwork0.2478 2438 -
all0.2522 2582 -
obs--98.62 %

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