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- PDB-2w1d: Structure determination of Aurora Kinase in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 2w1d
TitleStructure determination of Aurora Kinase in complex with inhibitor
ComponentsSERINE/THREONINE-PROTEIN KINASE 6
KeywordsTRANSFERASE / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / POLYMORPHISM / PHOSPHOPROTEIN / KINASE / CANCER / AURORA / INHIBITOR / 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 / chromosome passenger complex / histone H3S10 kinase activity / positive regulation of oocyte maturation / mitotic centrosome separation ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / chromosome passenger complex / histone H3S10 kinase activity / positive regulation of oocyte maturation / mitotic centrosome separation / pronucleus / germinal vesicle / protein localization to centrosome / meiotic spindle / anterior/posterior axis specification / neuron projection extension / spindle organization / centrosome localization / positive regulation of mitochondrial fission / mitotic spindle pole / spindle midzone / SUMOylation of DNA replication proteins / negative regulation of protein binding / regulation of G2/M transition of mitotic cell cycle / protein serine/threonine/tyrosine kinase activity / liver regeneration / centriole / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / molecular function activator activity / regulation of signal transduction by p53 class mediator / AURKA Activation by TPX2 / mitotic spindle organization / regulation of cytokinesis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / peptidyl-serine phosphorylation / regulation of protein stability / kinetochore / response to wounding / G2/M transition of mitotic cell cycle / spindle / spindle pole / mitotic spindle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / protein autophosphorylation / microtubule cytoskeleton / midbody / Regulation of TP53 Activity through Phosphorylation / basolateral plasma membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / postsynaptic density / ciliary basal body / protein heterodimerization activity / negative regulation of gene expression / cell division / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / centrosome / protein kinase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / glutamatergic synapse / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Aurora kinase A / Aurora kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
2-(1H-pyrazol-3-yl)-1H-benzimidazole / Aurora kinase A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.97 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)32,3422
Polymers32,1581
Non-polymers1841
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.008, 83.008, 169.719
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: KINASE DOMAIN, 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-L0D / 2-(1H-pyrazol-3-yl)-1H-benzimidazole


Mass: 184.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8N4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.33 % / 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: 2.97→54.85 Å / Num. obs: 7085 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 5.6

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Processing

SoftwareName: REFMAC / Version: 5.4.0069A / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.97→54.85 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.865 / SU B: 22.963 / SU ML: 0.421 / Cross valid method: THROUGHOUT / ESU R Free: 0.509 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.308 431 5.7 %RANDOM
Rwork0.236 ---
obs0.241 7085 98.1 %-
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: 69.06 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å2-0.82 Å20 Å2
2---1.63 Å20 Å2
3---2.45 Å2
Refinement stepCycle: LAST / Resolution: 2.97→54.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 14 0 2075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222127
X-RAY DIFFRACTIONr_bond_other_d0.0020.021501
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9662873
X-RAY DIFFRACTIONr_angle_other_deg1.7872.9943625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4245248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04322.913103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.34815377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1251518
X-RAY DIFFRACTIONr_chiral_restr0.0670.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212320
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02462
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_it2.13851250
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.55862014
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3996877
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7117.5859
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: 2.97→3.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.418 28
Rwork0.301 515

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