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- PDB-2xru: AURORA-A T288E COMPLEXED WITH PHA-828300 -

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Basic information

Entry
Database: PDB / ID: 2xru
TitleAURORA-A T288E COMPLEXED WITH PHA-828300
ComponentsSERINE/THREONINE-PROTEIN KINASE 6
KeywordsTRANSFERASE / NUCLEOTIDE-BINDING / KINASE / 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-400 / Aurora kinase A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBindi, S. / Fancelli, D. / Alli, C. / Berta, D. / Bertrand, J.A. / Cameron, A.D. / Cappella, P. / Carpinelli, P. / Cervi, G. / Croci, W. ...Bindi, S. / Fancelli, D. / Alli, C. / Berta, D. / Bertrand, J.A. / Cameron, A.D. / Cappella, P. / Carpinelli, P. / Cervi, G. / Croci, W. / D'Anello, M. / Forte, B. / LauraGiorgini, M. / Marsiglio, A. / Moll, J. / Pesenti, E. / Pittala, V. / Pulici, M. / Riccardi-Sirtori, F. / Roletto, F. / Soncini, C. / Storici, P. / Varasi, M. / Volpi, D. / Zugnoni, P. / Vianello, P.
CitationJournal: Bioorg.Med.Chem. / Year: 2010
Title: Thieno[3,2-C]Pyrazoles: A Novel Class of Aurora Inhibitors with Favorable Antitumor Activity.
Authors: Bindi, S. / Fancelli, D. / Alli, C. / Berta, D. / Bertrand, J.A. / Cameron, A.D. / Cappella, P. / Carpinelli, P. / Cervi, G. / Croci, V. / D'Anello, M. / Forte, B. / Laura Giorgini, M. / ...Authors: Bindi, S. / Fancelli, D. / Alli, C. / Berta, D. / Bertrand, J.A. / Cameron, A.D. / Cappella, P. / Carpinelli, P. / Cervi, G. / Croci, V. / D'Anello, M. / Forte, B. / Laura Giorgini, M. / Marsiglio, A. / Moll, J. / Pesenti, E. / Pittala, V. / Pulici, M. / Riccardi-Sirtori, F. / Roletto, F. / Soncini, C. / Storici, P. / Varasi, M. / Volpi, D. / Zugnoni, P. / Vianello, P.
History
DepositionSep 22, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4May 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)32,9002
Polymers32,3971
Non-polymers5031
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)82.467, 82.467, 165.453
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-RELATED KINASE 1 / HARK1


Mass: 32397.084 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 126-403 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-400 / 3-({[4-(4-METHYLPIPERAZIN-1-YL)PHENYL]CARBONYL}AMINO)-N-[(1R)-1-PHENYLPROPYL]-1H-THIENO[3,2-C]PYRAZOLE-5-CARBOXAMIDE / PHA-828300


Mass: 502.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H30N6O2S
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 288 TO GLU

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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: 2.74 Å3/Da / Density % sol: 54.7 % / Description: NONE
Crystal growpH: 5.6
Details: 15% PEG 5000 MME, 0.2 M LITHIUM SULFATE, 0.1 M SODIUM CITRATE PH 5.6 & 2 MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 17, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 7931 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Biso Wilson estimate: 95.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 34.6
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 3.2 / % possible all: 99.7

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.98 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 1264925.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.344 405 5.1 %RANDOM
Rwork0.247 ---
obs0.247 7878 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 73.1596 Å2 / ksol: 0.33917 e/Å3
Displacement parametersBiso mean: 97.1 Å2
Baniso -1Baniso -2Baniso -3
1--14.09 Å210.41 Å20 Å2
2---14.09 Å20 Å2
3---28.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.89 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2082 0 36 0 2118
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it13.511.5
X-RAY DIFFRACTIONc_mcangle_it20.962
X-RAY DIFFRACTIONc_scbond_it17.542
X-RAY DIFFRACTIONc_scangle_it24.852.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.082 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.628 59 4.7 %
Rwork0.476 1206 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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