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- PDB-3efw: Structure of AuroraA with pyridyl-pyrimidine urea inhibitor -

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Basic information

Entry
Database: PDB / ID: 3efw
TitleStructure of AuroraA with pyridyl-pyrimidine urea inhibitor
ComponentsSerine/threonine-protein kinase 6
KeywordsTransferase/Inhibitor / AuroraA / STK6_human / ATP-binding / Cell cycle / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Transferase-Inhibitor complex
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / germinal vesicle / spindle assembly involved in female meiosis I / axon hillock / spindle pole centrosome / positive regulation of oocyte maturation / pronucleus / chromosome passenger complex / histone serine kinase activity ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / germinal vesicle / spindle assembly involved in female meiosis I / axon hillock / spindle pole centrosome / positive regulation of oocyte maturation / pronucleus / chromosome passenger complex / histone serine kinase activity / meiotic spindle / centrosome localization / anterior/posterior axis specification / mitotic centrosome separation / protein localization to centrosome / neuron projection extension / positive regulation of mitochondrial fission / spindle organization / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / centriole / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / AURKA Activation by TPX2 / regulation of G2/M transition of mitotic cell cycle / positive regulation of mitotic nuclear division / regulation of signal transduction by p53 class mediator / protein serine/threonine/tyrosine kinase activity / cilium / regulation of cytokinesis / 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 / microtubule cytoskeleton / negative regulation of protein binding / response to wounding / spindle / regulation of protein stability / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / midbody / mitotic cell cycle / microtubule / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / peptidyl-serine phosphorylation / protein kinase activity / protein heterodimerization activity / centrosome / cell division / protein autophosphorylation / negative regulation of gene expression / protein serine/threonine kinase activity / protein serine kinase activity / protein serine/threonine kinase activity => GO:0004674 / ubiquitin protein ligase binding / protein phosphorylation / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain ...Aurora kinase A / Aurora kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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-AK8 / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsBellon, S.F. / Cee, V. / Hughes, P. / Geuns-Meyer, S. / Whittington, D.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Pyridyl-pyrimidine benzimidazole derivatives as potent, selective, and orally bioavailable inhibitors of Tie-2 kinase.
Authors: Cee, V.J. / Cheng, A.C. / Romero, K. / Bellon, S. / Mohr, C. / Whittington, D.A. / Bak, A. / Bready, J. / Caenepeel, S. / Coxon, A. / Deak, H.L. / Fretland, J. / Gu, Y. / Hodous, B.L. / ...Authors: Cee, V.J. / Cheng, A.C. / Romero, K. / Bellon, S. / Mohr, C. / Whittington, D.A. / Bak, A. / Bready, J. / Caenepeel, S. / Coxon, A. / Deak, H.L. / Fretland, J. / Gu, Y. / Hodous, B.L. / Huang, X. / Kim, J.L. / Lin, J. / Long, A.M. / Nguyen, H. / Olivieri, P.R. / Patel, V.F. / Wang, L. / Zhou, Y. / Hughes, P. / Geuns-Meyer, S.
History
DepositionSep 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references / Structure summary
Revision 1.3Jun 26, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase 6
B: Serine/threonine-protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2546
Polymers62,0732
Non-polymers1,1814
Water1,08160
1
A: Serine/threonine-protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6273
Polymers31,0371
Non-polymers5912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6273
Polymers31,0371
Non-polymers5912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)118.511, 125.448, 75.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 31036.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AURKA, AIK, ARK1, AURA, BTAK, STK15, STK6 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-AK8 / 1-[3-methyl-4-({3-[2-(methylamino)pyrimidin-4-yl]pyridin-2-yl}oxy)phenyl]-3-[3-(trifluoromethyl)phenyl]urea


Mass: 494.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H21F3N6O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 273 K / Method: vapor diffusion / pH: 4.6
Details: 0.1 M Sodium Acetate, 0.4 M Ammonium Sulfate, 15% PEG 4000, pH 4.6, VAPOR DIFFUSION, temperature 273K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 19, 2004 / Details: osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. all: 24589 / Num. obs: 22081 / % possible obs: 89.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 21.1
Reflection shellResolution: 2.29→2.41 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1453 / % possible all: 60.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→29.63 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.875 / SU B: 9.704 / SU ML: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.581 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29467 1110 5.1 %RANDOM
Rwork0.25808 ---
all0.26001 24339 --
obs0.26001 20740 85.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.15 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å20 Å2
2---1.36 Å20 Å2
3---2.73 Å2
Refinement stepCycle: LAST / Resolution: 2.29→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3846 0 82 60 3988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224025
X-RAY DIFFRACTIONr_angle_refined_deg1.0181.9945465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6075476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05823.425181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00715660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3411526
X-RAY DIFFRACTIONr_chiral_restr0.0590.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023062
X-RAY DIFFRACTIONr_nbd_refined0.1750.21657
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22742
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2153
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.211
X-RAY DIFFRACTIONr_mcbond_it0.4321.52483
X-RAY DIFFRACTIONr_mcangle_it0.78423856
X-RAY DIFFRACTIONr_scbond_it0.85431780
X-RAY DIFFRACTIONr_scangle_it1.3364.51609
LS refinement shellResolution: 2.29→2.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.501 33 -
Rwork0.31 793 -
obs-793 44.7 %

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