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- PDB-5aaf: Aurora A kinase bound to an imidazopyridine inhibitor (14a) -

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Basic information

Entry
Database: PDB / ID: 5aaf
TitleAurora A kinase bound to an imidazopyridine inhibitor (14a)
ComponentsAURORA KINASE A
KeywordsTRANSFERASE / AURORA-A / IMIDAZOPYRIDINE / AURORA KINASE / INHIBITOR
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 / positive regulation of oocyte maturation / pronucleus / 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 / positive regulation of oocyte maturation / pronucleus / mitotic centrosome separation / germinal vesicle / meiotic spindle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / spindle organization / positive regulation of mitochondrial fission / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / centriole / negative regulation of protein binding / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic cell cycle / positive regulation of mitotic nuclear division / mitotic spindle organization / AURKA Activation by TPX2 / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / ciliary basal body / liver regeneration / regulation of cytokinesis / molecular function activator activity / regulation of signal transduction by p53 class mediator / 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 / kinetochore / response to wounding / mitotic spindle / 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 / peptidyl-serine phosphorylation / midbody / protein autophosphorylation / basolateral plasma membrane / Regulation of TP53 Activity through Phosphorylation / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / postsynaptic density / protein phosphorylation / protein heterodimerization activity / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Aurora kinase A / Aurora kinase / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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-NL4 / Aurora kinase A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsMcIntyre, P.J. / Bayliss, R.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: 7-(Pyrazol-4-Yl)-3H-Imidazo[4,5-B]Pyridine-Based Derivatives for Kinase Inhibition: Co-Crystallisation Studies with Aurora-A Reveal Distinct Differences in the Orientation of the Pyrazole N1-Substituent.
Authors: Bavetsias, V. / Perez-Fuertes, Y. / Mcintyre, P.J. / Atrash, B. / Kosmopoulou, M. / O'Fee, L. / Burke, R. / Sun, C. / Faisal, A. / Bush, K. / Avery, S. / Henley, A. / Raynaud, F.I. / ...Authors: Bavetsias, V. / Perez-Fuertes, Y. / Mcintyre, P.J. / Atrash, B. / Kosmopoulou, M. / O'Fee, L. / Burke, R. / Sun, C. / Faisal, A. / Bush, K. / Avery, S. / Henley, A. / Raynaud, F.I. / Linardopoulos, S. / Bayliss, R. / Blagg, J.
History
DepositionJul 24, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / 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: AURORA KINASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3602
Polymers32,8851
Non-polymers4751
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)82.510, 82.510, 169.650
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 AURORA KINASE A / AURORA 2 / AURORA/IPL1-RELATED KINASE 1 / ARK-1 / AURORA-RELAT ED KINASE 1 / HARK1 / BREAST TUMOR- ...AURORA 2 / AURORA/IPL1-RELATED KINASE 1 / ARK-1 / AURORA-RELAT ED KINASE 1 / HARK1 / BREAST TUMOR-AMPLIFIED KINASE / SERINE/THREONIN E-PROTEIN KINASE 15 / SERINE/THREONINE-PROTEIN KINASE 6 / SERINE/THR EONINE-PROTEIN KINASE AURORA-A / AURORA A


Mass: 32884.656 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 122-403 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-NL4 / 3-((4-(6-chloro-2-(1,3-dimethyl-1H-pyrazol-4-yl)-3H-imidazo[4,5-b]pyridin-7-yl)-1H-pyrazol-1-yl)methyl)-N,N-dimethylbenzamide


Mass: 474.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23ClN8O

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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: 2.56 Å3/Da / Density % sol: 52.07 % / Description: NONE
Crystal growpH: 8.9
Details: 0.1 M TRIS PH 8.9, 0.2 M LITHIUM SULFATE, 30 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.78→65.85 Å / Num. obs: 9168 / % possible obs: 99.9 % / Observed criterion σ(I): 3.7 / Redundancy: 9.2 % / Biso Wilson estimate: 95.55 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23
Reflection shellResolution: 2.78→2.85 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BYI

4byi


Resolution: 2.78→54.65 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 32.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2871 439 4.8 %
Rwork0.2397 --
obs0.2422 9153 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.78→54.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 34 0 2037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042089
X-RAY DIFFRACTIONf_angle_d0.8042841
X-RAY DIFFRACTIONf_dihedral_angle_d14.073758
X-RAY DIFFRACTIONf_chiral_restr0.032310
X-RAY DIFFRACTIONf_plane_restr0.004363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7803-3.18250.39531290.31032830X-RAY DIFFRACTION100
3.1825-4.00950.37251580.28342837X-RAY DIFFRACTION100
4.0095-54.66020.24111520.21483047X-RAY DIFFRACTION100

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