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- PDB-2c6e: Aurora A kinase activated mutant (T287D) in complex with a 5- ami... -

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Basic information

Entry
Database: PDB / ID: 2c6e
TitleAurora A kinase activated mutant (T287D) in complex with a 5- aminopyrimidinyl quinazoline inhibitor
ComponentsSERINE/THREONINE-PROTEIN KINASE 6
KeywordsTRANSFERASE/INHIBITOR / TRANSFERASE-INHIBITOR COMPLEX / AURORA / KINASE / CANCER / ATP-BINDING / CELL CYCLE / NUCLEOTIDE- BINDING / PHOSPHORYLATION / SERINE/THREONINE-PROTEIN KINASE / TRANSFERASE
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 / liver regeneration / protein serine/threonine/tyrosine kinase activity / 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 / 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 / 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 / basolateral plasma membrane / Regulation of TP53 Activity through Phosphorylation / 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
Chem-HPM / Aurora kinase A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPauptit, R.A. / Pannifer, A.D. / Breed, J. / McMiken, H.H.J. / Rowsell, S. / Anderson, M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: Sar and Inhibitor Complex Structure Determination of a Novel Class of Potent and Specific Aurora Kinase Inhibitors.
Authors: Heron, N.M. / Anderson, M. / Blowers, D.P. / Breed, J. / Eden, J.M. / Green, S. / Hill, G.B. / Johnson, T. / Jung, F.H. / Mcmiken, H.H.J. / Mortlock, A.A. / Pannifer, A.D. / Pauptit, R.A. / ...Authors: Heron, N.M. / Anderson, M. / Blowers, D.P. / Breed, J. / Eden, J.M. / Green, S. / Hill, G.B. / Johnson, T. / Jung, F.H. / Mcmiken, H.H.J. / Mortlock, A.A. / Pannifer, A.D. / Pauptit, R.A. / Pink, J. / Roberts, N.J. / Rowsell, S.
History
DepositionNov 9, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)66,6044
Polymers65,5452
Non-polymers1,0592
Water1,838102
1
A: SERINE/THREONINE-PROTEIN KINASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3022
Polymers32,7731
Non-polymers5301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SERINE/THREONINE-PROTEIN KINASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3022
Polymers32,7731
Non-polymers5301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.603, 88.421, 67.832
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 32772.594 Da / Num. of mol.: 2 / Fragment: CATALYTIC KINASE DOMAIN, RESIDUES 123-401 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DS410(DE3) / References: UniProt: O14965, EC: 2.7.1.37
#2: Chemical ChemComp-HPM / N-{5-[(7-{[(2S)-2-HYDROXY-3-PIPERIDIN-1-YLPROPYL]OXY}-6-METHOXYQUINAZOLIN-4-YL)AMINO]PYRIMIDIN-2-YL}BENZAMIDE


Mass: 529.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H31N7O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPOSSIBLE ROLE IN CELL CYCLE REGULATION DURING ANAPHASE AND/OR TELOPHASE ENGINEERED RESIDUE IN CHAIN ...POSSIBLE ROLE IN CELL CYCLE REGULATION DURING ANAPHASE AND/OR TELOPHASE ENGINEERED RESIDUE IN CHAIN A, THR 288 TO ASP
Sequence detailsINITIAL GSHM IS REMAINDER OF THROMBIN-CLEAVED 6-HIS TAG. CONSTRUCT CONTAINS GSHM-(T287D)AURORAA(122-400).

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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: 2.6 Å3/Da / Density % sol: 62 %
Description: CRYSTAL TRANSLATED FOR DIFFERENT EXPOSURES. EPMR USED PARTIALLY-REFINED AURORA-ADPNP 2C6D TRIAL MODEL, WHICH WAS SOLVED USING PKA 1ATP
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 7, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.1→53 Å / Num. obs: 26294 / % possible obs: 72.5 % / Observed criterion σ(I): 0 / Redundancy: 1.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7
Reflection shellResolution: 2.1→2.25 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.1 / % possible all: 25.5

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Processing

Software
NameVersionClassification
CNX2000refinement
MOSFLMdata reduction
CCP4data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1ATP AND 2C6D

1atp

2c6d


Resolution: 2.1→53 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1269 3.5 %RANDOM
Rwork0.2 ---
obs-26287 --
Refinement stepCycle: LAST / Resolution: 2.1→53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4017 0 78 102 4197
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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