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- PDB-2xkc: Structure of Nek2 bound to aminopyrazine compound 14 -

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Basic information

Entry
Database: PDB / ID: 2xkc
TitleStructure of Nek2 bound to aminopyrazine compound 14
ComponentsSERINE/THREONINE-PROTEIN KINASE NEK2
KeywordsTRANSFERASE / CENTROSOME / MITOSIS
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 / blastocyst development / mitotic spindle assembly / 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 / blastocyst development / mitotic spindle assembly / 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 / APC-Cdc20 mediated degradation of Nek2A / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / 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 autophosphorylation / protein phosphatase binding / microtubule / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / ciliary basal body / cilium / protein phosphorylation / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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. ...: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-4VQ / Serine/threonine-protein kinase Nek2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMas-Droux, C. / Bayliss, R.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Aminopyrazine Inhibitors Binding to an Unusual Inactive Conformation of the Mitotic Kinase Nek2: Sar and Structural Characterization.
Authors: Whelligan, D.K. / Solanki, S. / Taylor, D. / Thomson, D.W. / Cheung, K.M. / Boxall, K. / Mas-Droux, C. / Barillari, C. / Burns, S. / Grummitt, C.G. / Collins, I. / Van Montfort, R.L. / ...Authors: Whelligan, D.K. / Solanki, S. / Taylor, D. / Thomson, D.W. / Cheung, K.M. / Boxall, K. / Mas-Droux, C. / Barillari, C. / Burns, S. / Grummitt, C.G. / Collins, I. / Van Montfort, R.L. / Aherne, G.W. / Bayliss, R. / Hoelder, S.
History
DepositionJul 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE NEK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2006
Polymers32,6621
Non-polymers5375
Water1,33374
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.110, 56.550, 73.610
Angle α, β, γ (deg.)90.00, 127.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE NEK2 / NEK2 / NEVER IN MITOSIS A-RELATED KINASE 2 / NIMA-RELATED PROTEIN KINASE 2 / NIMA-LIKE PROTEIN ...NEK2 / NEVER IN MITOSIS A-RELATED KINASE 2 / NIMA-RELATED PROTEIN KINASE 2 / NIMA-LIKE PROTEIN KINASE 1 / HSPK 21


Mass: 32662.479 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P51955, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-4VQ / 4-[3-amino-6-(3,4,5-trimethoxyphenyl)pyrazin-2-yl]-2-methylbenzoic acid


Mass: 395.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N3O5
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.09 % / Description: NONE
Crystal growDetails: 2-10% PEG8000, 100MM TRIS PH6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.2822
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2822 Å / Relative weight: 1
ReflectionResolution: 2.5→58.03 Å / Num. obs: 10970 / % possible obs: 97.1 % / Observed criterion σ(I): 6 / Redundancy: 3.2 % / Biso Wilson estimate: 31.54 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 7.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.7 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WQO

2wqo


Resolution: 2.5→31.029 Å / SU ML: 0.28 / σ(F): 0.04 / Phase error: 24.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 549 5.2 %
Rwork0.1866 --
obs0.1891 10480 92.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.248 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.6405 Å20 Å212.2854 Å2
2---15.815 Å20 Å2
3---13.1745 Å2
Refinement stepCycle: LAST / Resolution: 2.5→31.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 33 74 2056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032027
X-RAY DIFFRACTIONf_angle_d0.6112740
X-RAY DIFFRACTIONf_dihedral_angle_d16.811751
X-RAY DIFFRACTIONf_chiral_restr0.042300
X-RAY DIFFRACTIONf_plane_restr0.002346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.75140.2591220.19952260X-RAY DIFFRACTION85
2.7514-3.14930.27831310.18442487X-RAY DIFFRACTION93
3.1493-3.96640.22691490.17272558X-RAY DIFFRACTION96
3.9664-31.03110.20911470.18082626X-RAY DIFFRACTION95

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