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- PDB-6sgh: Nek2 kinase covalently bound to 2-arylamino-6-ethynylpurine inhib... -

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Basic information

Entry
Database: PDB / ID: 6sgh
TitleNek2 kinase covalently bound to 2-arylamino-6-ethynylpurine inhibitor 66
ComponentsSerine/threonine-protein kinase Nek2
KeywordsCELL CYCLE / "covalent inhibitor" kinase
Function / homology
Function and homology information


negative regulation of centriole-centriole cohesion / centrosome separation / regulation of attachment of spindle microtubules to kinetochore / regulation of mitotic centrosome separation / regulation of mitotic nuclear division / positive regulation of telomere maintenance / mitotic spindle assembly / blastocyst development / intercellular bridge / spindle assembly ...negative regulation of centriole-centriole cohesion / centrosome separation / regulation of attachment of spindle microtubules to kinetochore / regulation of mitotic centrosome separation / regulation of mitotic nuclear division / positive regulation of telomere maintenance / mitotic spindle assembly / blastocyst development / intercellular bridge / spindle assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / APC-Cdc20 mediated degradation of Nek2A / AURKA Activation by TPX2 / condensed nuclear chromosome / meiotic cell cycle / chromosome segregation / kinetochore / spindle pole / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / protein autophosphorylation / midbody / protein phosphatase binding / microtubule / protein phosphorylation / protein kinase activity / non-specific serine/threonine protein kinase / cilium / ciliary basal body / cell division / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleolus / protein-containing complex / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily ...: / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LCW / Serine/threonine-protein kinase Nek2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsRichards, M.W. / Mas-Droux, C.P. / Bayliss, R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC24461/A10285 United Kingdom
Cancer Research UKC24461/A23302 United Kingdom
CitationJournal: Rsc Med Chem / Year: 2020
Title: 2-Arylamino-6-ethynylpurines are cysteine-targeting irreversible inhibitors of Nek2 kinase.
Authors: Matheson, C.J. / Coxon, C.R. / Bayliss, R. / Boxall, K. / Carbain, B. / Fry, A.M. / Hardcastle, I.R. / Harnor, S.J. / Mas-Droux, C. / Newell, D.R. / Richards, M.W. / Sivaprakasam, M. / ...Authors: Matheson, C.J. / Coxon, C.R. / Bayliss, R. / Boxall, K. / Carbain, B. / Fry, A.M. / Hardcastle, I.R. / Harnor, S.J. / Mas-Droux, C. / Newell, D.R. / Richards, M.W. / Sivaprakasam, M. / Turner, D. / Griffin, R.J. / Golding, B.T. / Cano, C.
History
DepositionAug 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase Nek2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9572
Polymers32,6621
Non-polymers2941
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.020, 56.280, 74.010
Angle α, β, γ (deg.)90.000, 129.460, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Serine/threonine-protein kinase Nek2 / HSPK 21 / Never in mitosis A-related kinase 2 / NimA-related protein kinase 2 / NimA-like protein kinase 1


Mass: 32662.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEK2, NEK2A, NLK1 / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P51955, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-LCW / 2-[4-[(6-ethenyl-9~{H}-purin-2-yl)amino]phenyl]ethanamide


Mass: 294.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14N6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.87 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 50 mM Tris pH 8.5, 3% PEG 8000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3→57.14 Å / Num. obs: 6371 / % possible obs: 97.7 % / Redundancy: 2.3 % / Biso Wilson estimate: 48.39 Å2 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.104 / Net I/σ(I): 5.1
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 926 / Rpim(I) all: 0.336 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W5H

2w5h


Resolution: 3→57.14 Å / SU ML: 0.3811 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.8366
RfactorNum. reflection% reflection
Rfree0.2905 332 5.21 %
Rwork0.2266 --
obs0.23 6371 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.41 Å2
Refinement stepCycle: LAST / Resolution: 3→57.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 0 11 1859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321882
X-RAY DIFFRACTIONf_angle_d0.6582547
X-RAY DIFFRACTIONf_chiral_restr0.0425288
X-RAY DIFFRACTIONf_plane_restr0.0034324
X-RAY DIFFRACTIONf_dihedral_angle_d9.47831515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.780.32871570.24423012X-RAY DIFFRACTION97.87
3.78-57.140.27131750.2173027X-RAY DIFFRACTION96.47

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