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- PDB-2j4z: Structure of Aurora-2 in complex with PHA-680626 -

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Basic information

Entry
Database: PDB / ID: 2j4z
TitleStructure of Aurora-2 in complex with PHA-680626
ComponentsSERINE THREONINE-PROTEIN KINASE 6
KeywordsTRANSFERASE / PHOSPHORYLATION / NUCLEOTIDE-BINDING / KINASE / CELL CYCLE / ATP-BINDING / NUCLEOTIDE- BINDING / SERINE/THREONINE-PROTEIN KINASE / SERINE-THREONINE-PROTEIN KINASE
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / cilium disassembly / spindle pole centrosome / mitotic centrosome separation / histone H3S10 kinase activity / chromosome passenger complex / regulation of G2/M transition of mitotic cell cycle / germinal vesicle ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / cilium disassembly / spindle pole centrosome / mitotic centrosome separation / histone H3S10 kinase activity / chromosome passenger complex / regulation of G2/M transition of mitotic cell cycle / germinal vesicle / pronucleus / meiotic spindle organization / meiotic spindle / spindle organization / positive regulation of mitochondrial fission / mitotic spindle pole / spindle midzone / SUMOylation of DNA replication proteins / negative regulation of protein binding / liver regeneration / positive regulation of mitotic cell cycle / positive regulation of mitotic nuclear division / protein serine/threonine/tyrosine kinase activity / centriole / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / AURKA Activation by TPX2 / molecular function activator activity / regulation of signal transduction by p53 class mediator / mitotic spindle organization / regulation of cytokinesis / G2/M transition of mitotic cell cycle / response to wounding / regulation of protein stability / peptidyl-serine phosphorylation / 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 / kinetochore / spindle / microtubule cytoskeleton / mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / protein autophosphorylation / spindle pole / ciliary basal body / midbody / microtubule / Regulation of TP53 Activity through Phosphorylation / basolateral plasma membrane / cell division / protein kinase activity / protein phosphorylation / non-specific serine/threonine protein kinase / postsynaptic density / protein heterodimerization activity / negative regulation of gene expression / protein serine kinase activity / ubiquitin protein ligase binding / protein serine/threonine kinase activity / centrosome / protein kinase binding / 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
Chem-626 / ARSENIC / Aurora kinase A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCameron, A.D. / Izzo, G. / Storici, P. / Rusconi, L. / Fancelli, D. / Varasi, M. / Berta, D. / Bindi, S. / Forte, B. / Severino, D. ...Cameron, A.D. / Izzo, G. / Storici, P. / Rusconi, L. / Fancelli, D. / Varasi, M. / Berta, D. / Bindi, S. / Forte, B. / Severino, D. / Tonani, R. / Vianello, P.
CitationJournal: J. Med. Chem. / Year: 2006
Title: 1,4,5,6-tetrahydropyrrolo[3,4-c]pyrazoles: identification of a potent Aurora kinase inhibitor with a favorable antitumor kinase inhibition profile.
Authors: Fancelli, D. / Moll, J. / Varasi, M. / Bravo, R. / Artico, R. / Berta, D. / Bindi, S. / Cameron, A. / Candiani, I. / Cappella, P. / Carpinelli, P. / Croci, W. / Forte, B. / Giorgini, M.L. / ...Authors: Fancelli, D. / Moll, J. / Varasi, M. / Bravo, R. / Artico, R. / Berta, D. / Bindi, S. / Cameron, A. / Candiani, I. / Cappella, P. / Carpinelli, P. / Croci, W. / Forte, B. / Giorgini, M.L. / Klapwijk, J. / Marsiglio, A. / Pesenti, E. / Rocchetti, M. / Roletto, F. / Severino, D. / Soncini, C. / Storici, P. / Tonani, R. / Zugnoni, P. / Vianello, P.
History
DepositionSep 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 16, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_assembly
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.4Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 6
B: SERINE THREONINE-PROTEIN KINASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6767
Polymers70,5542
Non-polymers1,1225
Water3,495194
1
A: SERINE THREONINE-PROTEIN KINASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8764
Polymers35,2771
Non-polymers5983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SERINE THREONINE-PROTEIN KINASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8013
Polymers35,2771
Non-polymers5232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.127, 89.445, 94.037
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.73857, 0.24905, 0.62649), (0.28381, -0.72806, 0.62401), (0.61153, 0.63867, 0.46704)
Vector: 9.75534, 43.98392, -50.51562)

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Components

#1: Protein SERINE THREONINE-PROTEIN KINASE 6 / SERINE/THREONINE KINASE 15 / AURORA/IPL1-RELATED KINASE 1 / AURORA-RELATED KINASE 1 / HARK1 / ...SERINE/THREONINE KINASE 15 / AURORA/IPL1-RELATED KINASE 1 / AURORA-RELATED KINASE 1 / HARK1 / AURORA-A / BREAST-TUMOR-AMPLIFIED KINASE


Mass: 35277.195 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 100-403
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, EC: 2.7.1.37, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-626 / 4-(4-METHYLPIPERAZIN-1-YL)-N-[5-(2-THIENYLACETYL)-1,5-DIHYDROPYRROLO[3,4-C]PYRAZOL-3-YL]BENZAMIDE


Mass: 448.541 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H24N6O2S
#3: Chemical ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: As
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGP IS PRESENT AT START DUE TO CLONING ARTIFACT

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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: 2.5 Å3/Da / Density % sol: 0.36 %
Crystal growpH: 6.5
Details: 30% PEG 5000MME, 0.2M SODIUM ACETATE 0.1M SODIUM CACODYLATE PH 6.5, 2MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 28, 2002
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 41492 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
CNX2002refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BMC

2bmc


Resolution: 2→29.58 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2037 5 %RANDOM
Rwork0.214 ---
obs-41144 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.6533 Å2 / ksol: 0.373048 e/Å3
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1-4.48 Å20 Å20 Å2
2---5.27 Å20 Å2
3---0.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4365 0 67 194 4626
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.422
X-RAY DIFFRACTIONc_scbond_it2.362
X-RAY DIFFRACTIONc_scangle_it3.642.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6 /
Rfactor% reflection
Rfree0.288 4.9 %
Rwork0.245 -
obs-100 %
Xplor fileSerial no: 1 / Param file: PROTEIN.PARAM / Topol file: 626.TOP

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