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- PDB-5m51: Nek2 bound to arylaminopurine compound 8 -

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Basic information

Entry
Database: PDB / ID: 5m51
TitleNek2 bound to arylaminopurine compound 8
ComponentsSerine/threonine-protein kinase Nek2
KeywordsTransferase/Inhibitor / Protein kinase / Inhibitor / Centrosome separation / Transferase-Inhibitor complex
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 capping / blastocyst development / mitotic spindle assembly / 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 capping / blastocyst development / mitotic spindle assembly / 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 / positive regulation of telomere maintenance via telomerase / 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 / midbody / protein phosphatase binding / protein autophosphorylation / microtubule / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleolus / protein-containing complex / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / 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 domain profile. ...: / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-NU6 / Serine/threonine-protein kinase Nek2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsBayliss, R. / Yeoh, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC24461/A10285 United Kingdom
CitationJournal: Oncotarget / Year: 2017
Title: Structure-guided design of purine-based probes for selective Nek2 inhibition.
Authors: Coxon, C.R. / Wong, C. / Bayliss, R. / Boxall, K. / Carr, K.H. / Fry, A.M. / Hardcastle, I.R. / Matheson, C.J. / Newell, D.R. / Sivaprakasam, M. / Thomas, H. / Turner, D. / Yeoh, S. / Wang, ...Authors: Coxon, C.R. / Wong, C. / Bayliss, R. / Boxall, K. / Carr, K.H. / Fry, A.M. / Hardcastle, I.R. / Matheson, C.J. / Newell, D.R. / Sivaprakasam, M. / Thomas, H. / Turner, D. / Yeoh, S. / Wang, L.Z. / Griffin, R.J. / Golding, B.T. / Cano, C.
History
DepositionOct 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2May 3, 2017Group: Database references
Revision 1.3Jan 17, 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: Serine/threonine-protein kinase Nek2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0292
Polymers32,6621
Non-polymers3661
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.717, 73.736, 75.076
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Production host: Escherichia coli (E. coli)
References: UniProt: P51955, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-NU6 / 3-[[6-(cyclohexylmethoxy)-9~{H}-purin-2-yl]amino]benzamide


Mass: 366.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3 % PEG 8000, 50 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.899→73.7 Å / Num. obs: 25458 / % possible obs: 99.8 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.8
Reflection shellResolution: 1.899→2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 3.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W5A

2w5a


Resolution: 1.899→52.607 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.8
RfactorNum. reflection% reflection
Rfree0.2567 1280 5.04 %
Rwork0.222 --
obs0.2237 25394 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.899→52.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 27 99 2187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082133
X-RAY DIFFRACTIONf_angle_d1.0572888
X-RAY DIFFRACTIONf_dihedral_angle_d16.151798
X-RAY DIFFRACTIONf_chiral_restr0.048317
X-RAY DIFFRACTIONf_plane_restr0.005369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.899-1.97510.30751400.28822620X-RAY DIFFRACTION99
1.9751-2.0650.27851500.24032631X-RAY DIFFRACTION100
2.065-2.17380.26461410.22412652X-RAY DIFFRACTION100
2.1738-2.310.25071410.22242625X-RAY DIFFRACTION100
2.31-2.48840.28781550.22082658X-RAY DIFFRACTION100
2.4884-2.73880.25761380.22622682X-RAY DIFFRACTION100
2.7388-3.1350.25641390.23292690X-RAY DIFFRACTION100
3.135-3.94960.25511220.22072746X-RAY DIFFRACTION100
3.9496-52.6270.24181540.20962810X-RAY DIFFRACTION99

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