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- PDB-2w1f: Structure determination of Aurora Kinase in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 2w1f
TitleStructure determination of Aurora Kinase in complex with inhibitor
ComponentsSERINE/THREONINE-PROTEIN KINASE 6
KeywordsTRANSFERASE / CANCER / AURORA / KINASE / INHIBITOR / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / POLYMORPHISM / PHOSPHOPROTEIN / CELL CYCLE
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 / histone H3S10 kinase activity / chromosome passenger complex / positive regulation of oocyte maturation / pronucleus ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / histone H3S10 kinase activity / chromosome passenger complex / positive regulation of oocyte maturation / pronucleus / mitotic centrosome separation / meiotic spindle / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / spindle organization / neuron projection extension / positive regulation of mitochondrial fission / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / protein serine/threonine/tyrosine kinase activity / centriole / AURKA Activation by TPX2 / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / ciliary basal body / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / negative regulation of protein binding / 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 / kinetochore / response to wounding / spindle / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / peptidyl-serine phosphorylation / basolateral plasma membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / microtubule / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / protein phosphorylation / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / 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-L0F / Aurora kinase A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsHoward, S. / Berdini, V. / Boulstridge, J.A. / Carr, M.G. / Cross, D.M. / Curry, J. / Devine, L.A. / Early, T.R. / Fazal, L. / Gill, A.L. ...Howard, S. / Berdini, V. / Boulstridge, J.A. / Carr, M.G. / Cross, D.M. / Curry, J. / Devine, L.A. / Early, T.R. / Fazal, L. / Gill, A.L. / Heathcote, M. / Maman, S. / Matthews, J.E. / McMenamin, R.L. / Navarro, E.F. / O'Brien, M.A. / O'Reilly, M. / Rees, D.C. / Reule, M. / Tisi, D. / Williams, G. / Vinkovic, M. / Wyatt, P.G.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Fragment-Based Discovery of the Pyrazol-4-Yl Urea (at9283), a Multitargeted Kinase Inhibitor with Potent Aurora Kinase Activity.
Authors: Howard, S. / Berdini, V. / Boulstridge, J.A. / Carr, M.G. / Cross, D.M. / Curry, J. / Devine, L.A. / Early, T.R. / Fazal, L. / Gill, A.L. / Heathcote, M. / Maman, S. / Matthews, J.E. / ...Authors: Howard, S. / Berdini, V. / Boulstridge, J.A. / Carr, M.G. / Cross, D.M. / Curry, J. / Devine, L.A. / Early, T.R. / Fazal, L. / Gill, A.L. / Heathcote, M. / Maman, S. / Matthews, J.E. / Mcmenamin, R.L. / Navarro, E.F. / O'Brien, M.A. / O'Reilly, M. / Rees, D.C. / Reule, M. / Tisi, D. / Williams, G. / Vinkovic, M. / Wyatt, P.G.
History
DepositionOct 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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)32,4612
Polymers32,1581
Non-polymers3031
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.527, 82.527, 168.443
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 / AURORA KINASE A / SERINE/THREONINE KINASE 15 / AURORA/IPL1-RELATED KINASE 1 / BREAST TUMOR- ...AURORA KINASE A / SERINE/THREONINE KINASE 15 / AURORA/IPL1-RELATED KINASE 1 / BREAST TUMOR-AMPLIFIED KINASE / AURORA A / AURORA-A / AURORA-RELATED KINASE 1 / HARK1


Mass: 32157.941 Da / Num. of mol.: 1 / Fragment: RESIDUES 122-389
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET 23A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-L0F / N-[3-(1H-BENZIMIDAZOL-2-YL)-1H-PYRAZOL-4-YL]BENZAMIDE


Mass: 303.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13N5O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.25 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.91
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.85→65.79 Å / Num. obs: 7793 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 5

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Processing

SoftwareName: REFMAC / Version: 5.4.0069A / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→65.79 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.832 / SU B: 19.947 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.535 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.348 434 5.3 %RANDOM
Rwork0.241 ---
obs0.246 7793 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 76.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å2-0.47 Å20 Å2
2---0.93 Å20 Å2
3---1.4 Å2
Refinement stepCycle: LAST / Resolution: 2.85→65.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2080 0 23 30 2133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222158
X-RAY DIFFRACTIONr_bond_other_d0.0020.021518
X-RAY DIFFRACTIONr_angle_refined_deg1.291.962917
X-RAY DIFFRACTIONr_angle_other_deg1.542.9893665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0045251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54622.926108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.04415380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3841518
X-RAY DIFFRACTIONr_chiral_restr0.0680.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212366
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02472
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_it2.19651261
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.66362033
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5076897
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8597.5884
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: 2.85→2.92 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.349 26
Rwork0.302 555

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