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- PDB-3m11: Crystal Structure of Aurora A Kinase complexed with inhibitor -

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Basic information

Entry
Database: PDB / ID: 3m11
TitleCrystal Structure of Aurora A Kinase complexed with inhibitor
ComponentsSerine/threonine-protein kinase 6Serine/threonine-specific protein kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Aurora kinase inhibitor / X-ray co-crystal analysis / Structure-based drug design / ATP-binding / Cell cycle / Cytoskeleton / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / 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 / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / positive regulation of mitochondrial fission / spindle organization / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic cell cycle / AURKA Activation by TPX2 / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of mitotic nuclear division / ciliary basal body / negative regulation of protein binding / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / 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 / spindle / kinetochore / response to wounding / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / microtubule / postsynaptic density / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / cell division / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / 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 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-AKI / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsWu, J.S. / Leou, J.S. / Coumar, M.S. / Hsieh, H.P. / Wu, S.Y.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Fast-forwarding hit to lead: aurora and epidermal growth factor receptor kinase inhibitor lead identification
Authors: Coumar, M.S. / Chu, C.Y. / Lin, C.W. / Shiao, H.Y. / Ho, Y.L. / Reddy, R. / Lin, W.H. / Chen, C.H. / Peng, Y.H. / Leou, J.S. / Lien, T.W. / Huang, C.T. / Fang, M.Y. / Wu, S.H. / Wu, J.S. / ...Authors: Coumar, M.S. / Chu, C.Y. / Lin, C.W. / Shiao, H.Y. / Ho, Y.L. / Reddy, R. / Lin, W.H. / Chen, C.H. / Peng, Y.H. / Leou, J.S. / Lien, T.W. / Huang, C.T. / Fang, M.Y. / Wu, S.H. / Wu, J.S. / Chittimalla, S.K. / Song, J.S. / Hsu, J.T. / Wu, S.Y. / Liao, C.C. / Chao, Y.S. / Hsieh, H.P.
History
DepositionMar 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)32,8852
Polymers32,3591
Non-polymers5261
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)82.266, 82.266, 170.283
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-102-

HOH

21A-107-

HOH

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Components

#1: Protein Serine/threonine-protein kinase 6 / Serine/threonine-specific protein kinase / Aurora kinase A / Serine/threonine-protein kinase aurora-A / Serine/threonine-protein kinase 15 / ...Aurora kinase A / Serine/threonine-protein kinase aurora-A / Serine/threonine-protein kinase 15 / Aurora/IPL1-related kinase 1 / Aurora-related kinase 1 / ARK-1 / hARK1 / Breast tumor-amplified kinase


Mass: 32359.123 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: T288D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-AKI / 1-(4-{2-[(5,6-diphenylfuro[2,3-d]pyrimidin-4-yl)amino]ethyl}phenyl)-3-phenylurea


Mass: 525.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H27N5O2
#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: 2.57 Å3/Da / Density % sol: 52.14 % / Mosaicity: 1.069 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG400, 0.1mM ammonia sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.75→30 Å / Num. all: 8964 / Num. obs: 8896 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.046 / Χ2: 1.054 / Net I/σ(I): 24.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.75-2.8590.3448631.08194.9
2.85-2.968.90.2338651.08795.2
2.96-3.190.1828681.08595.7
3.1-3.268.90.1228661.08294.9
3.26-3.468.90.0778691.03194
3.46-3.738.60.0568881.0194.3
3.73-4.118.40.0449101.04396.7
4.11-4.78.60.0419111.06897.4
4.7-5.918.70.0389451.03696.1
5.91-308.70.0289791.02391.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.25 Å28.38 Å
Translation3.25 Å28.38 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FDN

3fdn


Resolution: 2.75→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.321 / WRfactor Rwork: 0.238 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.737 / SU B: 17.537 / SU ML: 0.348 / SU Rfree: 0.435 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.435 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.299 419 4.7 %RANDOM
Rwork0.217 ---
obs0.221 8896 94.73 %-
all-8964 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.58 Å2 / Biso mean: 69.047 Å2 / Biso min: 40.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å2-0.35 Å20 Å2
2---0.7 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 40 100 2202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222161
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9832931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4255254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26523.333102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.81115354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5961515
X-RAY DIFFRACTIONr_chiral_restr0.0890.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021666
X-RAY DIFFRACTIONr_nbd_refined0.2340.21050
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21444
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2134
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3450.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.213
X-RAY DIFFRACTIONr_mcbond_it0.7591.51307
X-RAY DIFFRACTIONr_mcangle_it1.37522050
X-RAY DIFFRACTIONr_scbond_it1.3493977
X-RAY DIFFRACTIONr_scangle_it2.2284.5881
LS refinement shellResolution: 2.754→2.825 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 31 -
Rwork0.276 603 -
all-634 -
obs--95.05 %

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