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- PDB-3daj: Crystal structure of Aurora A complexed with an inhibitor discove... -

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Basic information

Entry
Database: PDB / ID: 3daj
TitleCrystal structure of Aurora A complexed with an inhibitor discovered through site-directed dynamic tethering
Componentsserine/threonine kinase 6Serine/threonine-specific protein kinase
KeywordsTRANSFERASE / Protein-small molecule inhibitor complex / Kinase
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / 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 / AURKA Activation by TPX2 / meiotic spindle organization / Regulation of PLK1 Activity at G2/M Transition / Regulation of TP53 Activity through Phosphorylation / axon hillock / spindle assembly involved in female meiosis I ...Interaction between PHLDA1 and AURKA / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / 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 / AURKA Activation by TPX2 / meiotic spindle organization / Regulation of PLK1 Activity at G2/M Transition / Regulation of TP53 Activity through Phosphorylation / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / meiotic spindle / mitotic centrosome separation / centrosome cycle / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / microtubule organizing center / centrosome localization / neuron projection extension / positive regulation of mitochondrial fission / spindle organization / mitotic spindle pole / spindle midzone / centriole / positive regulation of mitotic cell cycle / mitotic spindle organization / ciliary basal body / meiotic cell cycle / regulation of cytokinesis / molecular function activator activity / liver regeneration / spindle microtubule / regulation of protein stability / mitotic spindle / microtubule cytoskeleton organization / kinetochore / spindle pole / response to wounding / microtubule cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / cell division / phosphorylation / negative regulation of gene expression / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
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 ...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-FXG / Aurora kinase A / Aurora kinase A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHe, M.M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Discovery of an Aurora kinase inhibitor through site-specific dynamic combinatorial chemistry.
Authors: Cancilla, M.T. / He, M.M. / Viswanathan, N. / Simmons, R.L. / Taylor, M. / Fung, A.D. / Cao, K. / Erlanson, D.A.
History
DepositionMay 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: serine/threonine kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9872
Polymers31,5631
Non-polymers4241
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.932, 84.932, 77.025
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein serine/threonine kinase 6 / Serine/threonine-specific protein kinase / Aurora-A


Mass: 31563.158 Da / Num. of mol.: 1 / Mutation: N173G, K227R, T287D, M289L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aurka, Stk6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8C3H8, UniProt: P97477*PLUS
#2: Chemical ChemComp-FXG / N-butyl-3-{[6-(9H-purin-6-ylamino)hexanoyl]amino}benzamide


Mass: 423.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H29N7O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.8-2.2 M diammonium hydrogen phosphate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 19365 / Redundancy: 4.2 % / Rsym value: 8.8 / Net I/σ(I): 1.3
Reflection shellResolution: 2→2.069 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.2 / Rsym value: 48.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.894 / SU B: 4.773 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28355 987 5.1 %RANDOM
Rwork0.25135 ---
obs0.253 18287 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å20 Å2
2---1.66 Å20 Å2
3---3.31 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 31 100 2132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222083
X-RAY DIFFRACTIONr_angle_refined_deg0.8561.9732818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.185242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5722.673101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78915349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2331518
X-RAY DIFFRACTIONr_chiral_restr0.0540.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021587
X-RAY DIFFRACTIONr_nbd_refined0.1530.2897
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21414
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0850.2130
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0690.219
X-RAY DIFFRACTIONr_mcbond_it1.172.51259
X-RAY DIFFRACTIONr_mcangle_it1.9651961
X-RAY DIFFRACTIONr_scbond_it1.1372.5957
X-RAY DIFFRACTIONr_scangle_it1.875857
LS refinement shellResolution: 2→2.069 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.295 88 -
Rwork0.268 1610 -
obs--90.08 %

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