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- PDB-7fic: Reversible lysine-targeted probes reveal residence time-based kin... -

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Basic information

Entry
Database: PDB / ID: 7fic
TitleReversible lysine-targeted probes reveal residence time-based kinase selectivity in vivo
ComponentsAurora kinase A
KeywordsCELL CYCLE / Reversible lysine-targeted inhibitors / kinase
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 / 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-5YZ / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsCraven, G.B. / Wan, X.B. / Taunton, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privatePfizer United States
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Reversible lysine-targeted probes reveal residence time-based kinase selectivity.
Authors: Yang, T. / Cuesta, A. / Wan, X. / Craven, G.B. / Hirakawa, B. / Khamphavong, P. / May, J.R. / Kath, J.C. / Lapek Jr., J.D. / Niessen, S. / Burlingame, A.L. / Carelli, J.D. / Taunton, J.
History
DepositionJul 31, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)31,3115
Polymers30,7181
Non-polymers5934
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.950, 87.950, 76.824
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-404-

CL

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Components

#1: Protein Aurora kinase A / / Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / hARK1 / Breast tumor- ...Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-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: 30718.256 Da / Num. of mol.: 1 / Mutation: C290A
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 BL21(DE3) (bacteria)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-5YZ / 6-[(5-cyclopropyl-1~{H}-pyrazol-3-yl)amino]-2-[4-[(3-methyl-4-oxidanyl-phenyl)methyl]piperazin-1-yl]-~{N}-prop-2-ynyl-pyrimidine-4-carboxamide


Mass: 486.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H30N8O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M lithium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11685 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11685 Å / Relative weight: 1
ReflectionResolution: 2.32→76.21 Å / Num. obs: 15223 / % possible obs: 99.9 % / Redundancy: 19.5 % / Biso Wilson estimate: 85.49 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.011 / Rrim(I) all: 0.05 / Net I/σ(I): 25.5
Reflection shellResolution: 2.32→2.403 Å / Rmerge(I) obs: 2.109 / Num. unique obs: 1516 / CC1/2: 0.642 / Rrim(I) all: 2.163

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PHENIX1.19.1refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CEG

4ceg


Resolution: 2.32→76.17 Å / SU ML: 0.4137 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.6528
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.274 779 5.13 %
Rwork0.2356 27281 -
obs0.2375 15219 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.24 Å2
Refinement stepCycle: LAST / Resolution: 2.32→76.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 39 6 2024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00982081
X-RAY DIFFRACTIONf_angle_d1.30492832
X-RAY DIFFRACTIONf_chiral_restr0.0678310
X-RAY DIFFRACTIONf_plane_restr0.0114361
X-RAY DIFFRACTIONf_dihedral_angle_d17.5148746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.40.32941160.36012509X-RAY DIFFRACTION99.51
2.4-2.480.35821160.34172485X-RAY DIFFRACTION99.69
2.48-2.580.4989940.41492558X-RAY DIFFRACTION100
2.58-2.70.38821100.37442453X-RAY DIFFRACTION99.84
2.7-2.840.3911640.33912486X-RAY DIFFRACTION100
2.84-3.020.32751900.33312396X-RAY DIFFRACTION99.61
3.02-3.250.34731500.34482469X-RAY DIFFRACTION100
3.25-3.570.31971540.29672420X-RAY DIFFRACTION99.69
3.58-4.10.2951420.23832502X-RAY DIFFRACTION100
4.1-5.160.20861320.18762498X-RAY DIFFRACTION100
5.16-76.170.23121070.1822505X-RAY DIFFRACTION99.89

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