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- PDB-4zts: Human Aurora A catalytic domain bound to FK1142 -

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Basic information

Entry
Database: PDB / ID: 4zts
TitleHuman Aurora A catalytic domain bound to FK1142
ComponentsAurora kinase A
KeywordsTRANSFERASE / 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 / histone H3S10 kinase activity / chromosome passenger complex / positive regulation of oocyte maturation / pronucleus ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / histone H3S10 kinase activity / chromosome passenger complex / positive regulation of oocyte maturation / pronucleus / mitotic centrosome separation / meiotic spindle / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / spindle organization / neuron projection extension / positive regulation of mitochondrial fission / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / protein serine/threonine/tyrosine kinase activity / centriole / AURKA Activation by TPX2 / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / ciliary basal body / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / negative regulation of protein binding / 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 / kinetochore / response to wounding / 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 / midbody / peptidyl-serine phosphorylation / basolateral plasma membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / microtubule / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / protein phosphorylation / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / 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-4RK / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMarcaida, M.J. / Kilchmann, F. / Schick, T. / Reymond, J.L.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science FoundationPMPDP3_139609 Switzerland
Swiss National Science Foundation51AU40_125781 Switzerland
CitationJournal: J.Med.Chem. / Year: 2016
Title: Discovery of a Selective Aurora A Kinase Inhibitor by Virtual Screening.
Authors: Kilchmann, F. / Marcaida, M.J. / Kotak, S. / Schick, T. / Boss, S.D. / Awale, M. / Gonczy, P. / Reymond, J.L.
History
DepositionMay 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)33,5503
Polymers32,9491
Non-polymers6012
Water18010
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-6 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.380, 82.380, 188.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-605-

HOH

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Components

#1: Protein Aurora kinase A / Aurora 2 / Aurora/IPL1-related kinase 1 / hARK1 / Breast tumor-amplified kinase / Serine/threonine- ...Aurora 2 / Aurora/IPL1-related kinase 1 / hARK1 / Breast tumor-amplified kinase / Serine/threonine-protein kinase 15 / Serine/threonine-protein kinase 6 / Serine/threonine-protein kinase aurora-A


Mass: 32948.781 Da / Num. of mol.: 1 / Fragment: residues 122-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6
Production host: Escherichia coli (E. coli)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-4RK / (2Z,5Z)-2-[(4-ethylphenyl)imino]-3-methyl-5-[(2-{[4-(1H-tetrazol-5-yl)phenyl]amino}pyridin-4-yl)methylidene]-1,3-thiazolidin-4-one


Mass: 482.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H22N8OS
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 5% MPD, 0.1 M Hepes pH 7.5, 10% PEG 10K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→47.2 Å / Num. obs: 8932 / % possible obs: 99.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OL5

1ol5


Resolution: 2.9→47.17 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.944 / SU B: 35.307 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R: 1.728 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 447 5 %RANDOM
Rwork0.21105 ---
obs0.21296 8484 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.503 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å2-0.9 Å20 Å2
2---1.8 Å20 Å2
3---5.83 Å2
Refinement stepCycle: 1 / Resolution: 2.9→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 43 10 2054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192098
X-RAY DIFFRACTIONr_bond_other_d0.0010.021983
X-RAY DIFFRACTIONr_angle_refined_deg1.0341.9872846
X-RAY DIFFRACTIONr_angle_other_deg0.71734541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3835247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09823.15895
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01915346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3111514
X-RAY DIFFRACTIONr_chiral_restr0.0580.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212329
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02499
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3335.071994
X-RAY DIFFRACTIONr_mcbond_other1.3345.071993
X-RAY DIFFRACTIONr_mcangle_it2.3287.6041239
X-RAY DIFFRACTIONr_mcangle_other2.3277.6031240
X-RAY DIFFRACTIONr_scbond_it1.3525.2691101
X-RAY DIFFRACTIONr_scbond_other1.3525.2711102
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3537.8541607
X-RAY DIFFRACTIONr_long_range_B_refined4.40241.6792389
X-RAY DIFFRACTIONr_long_range_B_other4.40141.6952390
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.901→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 32 -
Rwork0.314 599 -
obs--97.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.4659-0.9911.67573.73810.78933.3315-0.33060.82871.2115-0.17680.0521-0.0792-0.71970.72760.27850.3005-0.2495-0.06870.27450.15520.37890.4578-21.0123-11.6804
25.9274-1.65210.91281.5169-0.82192.5607-0.10220.53260.11430.0734-0.0338-0.08140.0267-0.08960.1360.1395-0.1041-0.02750.2623-0.05190.173911.8142-36.9992-7.7483
34.60550.61940.98442.87480.80223.1723-0.22830.7252-0.0659-0.08390.065-0.1284-0.06880.22480.16330.09780.01790.05850.211-0.00310.107125.0072-37.0327-2.3488
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A127 - 216
2X-RAY DIFFRACTION2A217 - 275
3X-RAY DIFFRACTION3A276 - 388

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