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- PDB-7ayh: Crystal structure of Aurora A in complex with 7-(2-Anilinopyrimid... -

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Basic information

Entry
Database: PDB / ID: 7ayh
TitleCrystal structure of Aurora A in complex with 7-(2-Anilinopyrimidin-4-yl)-1-benzazepin-2-one derivative (compound 2c)
ComponentsAurora kinase A
KeywordsTRANSFERASE / kinase / kinase inhibitor / aurora kinase / stk6 / Structural Genomics / Structural Genomics Consortium / SGC
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 / protein serine/threonine/tyrosine kinase activity / liver regeneration / 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 / 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 / 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 / Regulation of TP53 Activity through Phosphorylation / basolateral plasma membrane / 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 / 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
Similarity search - Domain/homology
Chem-S9H / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChaikuad, A. / Karatas, M. / Kunick, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Molecules / Year: 2021
Title: 7-(2-Anilinopyrimidin-4-yl)-1-benzazepin-2-ones Designed by a "Cut and Glue" Strategy Are Dual Aurora A/VEGF-R Kinase Inhibitors.
Authors: Karatas, M. / Chaikuad, A. / Berger, B. / Kubbutat, M.H.G. / Totzke, F. / Knapp, S. / Kunick, C.
History
DepositionNov 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 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)33,3092
Polymers32,9491
Non-polymers3601
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.362, 83.362, 168.208
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 / 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
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
Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-S9H / 7-[2-[(4-methoxyphenyl)amino]pyrimidin-4-yl]-1,3,4,5-tetrahydro-1-benzazepin-2-one


Mass: 360.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N4O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 51.96 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 24% PEG 3350, 0.2 M sodium malonate pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99986 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionResolution: 2.8→44.28 Å / Num. obs: 9066 / % possible obs: 99.9 % / Redundancy: 8.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.018 / Rrim(I) all: 0.051 / Net I/σ(I): 19.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.8-2.9590.9752.112790.8180.3551.077100
8.86-44.287.10.0313450.9980.0120.03498.4

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ONE

5one


Resolution: 2.8→44.28 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.899 / SU B: 50.894 / SU ML: 0.446 / SU R Cruickshank DPI: 1.6239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.624 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3126 466 5.1 %RANDOM
Rwork0.2726 ---
obs0.2746 8590 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 224.55 Å2 / Biso mean: 132.566 Å2 / Biso min: 79.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0.27 Å20 Å2
2---0.53 Å2-0 Å2
3---1.72 Å2
Refinement stepCycle: final / Resolution: 2.8→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 27 0 2031
Biso mean--111.96 --
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0142083
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171866
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.6542825
X-RAY DIFFRACTIONr_angle_other_deg0.91.6414353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0765248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80821.441111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97615346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4781515
X-RAY DIFFRACTIONr_chiral_restr0.0640.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022442
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02402
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 34 -
Rwork0.379 605 -
all-639 -
obs--99.84 %
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)
12.23872.51551.90383.66682.59651.8847-0.0514-0.40790.9708-0.3061-0.36860.259-0.283-0.43770.42010.48960.37070.22390.84810.20491.4386-4.0514-22.743812.6378
26.0065-0.20931.64563.2756-0.24343.3327-0.2079-0.82820.04650.2752-0.0060.2756-0.1164-0.35950.21380.04380.07860.07120.30520.17470.245-22.7-37.63814.927
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A125 - 205
2X-RAY DIFFRACTION2A206 - 390

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