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- PDB-2xk3: Structure of Nek2 bound to Aminopyrazine compound 35 -

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Basic information

Entry
Database: PDB / ID: 2xk3
TitleStructure of Nek2 bound to Aminopyrazine compound 35
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 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-XK3 / Serine/threonine-protein kinase Nek2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)33,0654
Polymers32,6621
Non-polymers4023
Water3,189177
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.030, 57.090, 81.410
Angle α, β, γ (deg.)90.00, 133.50, 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-XK3 / 4-[3-AMINO-6-(3-ETHYLTHIOPHEN-2-YL)PYRAZIN-2-YL]CYCLOHEXANE-1-CARBOXYLIC ACID


Mass: 331.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N3O2S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.61 Å3/Da / Density % sol: 52.8 % / 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: 0.9763
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→50.3 Å / Num. obs: 13956 / % possible obs: 81.2 % / Observed criterion σ(I): 6 / Redundancy: 3.4 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 8.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 2.4 / % possible all: 99.1

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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: 2.2→19.684 Å / SU ML: 0.27 / σ(F): 0.03 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2379 710 5.4 %
Rwork0.1847 --
obs0.1876 13232 76.97 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.127 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0768 Å2-0 Å2-7.2548 Å2
2---8.038 Å20 Å2
3---9.1148 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1978 0 25 177 2180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092060
X-RAY DIFFRACTIONf_angle_d1.0512784
X-RAY DIFFRACTIONf_dihedral_angle_d17.73774
X-RAY DIFFRACTIONf_chiral_restr0.077307
X-RAY DIFFRACTIONf_plane_restr0.008354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2002-2.36980.26471570.22852818X-RAY DIFFRACTION88
2.3698-2.60780.244960.21331747X-RAY DIFFRACTION91
2.6078-2.9840.2292940.1871542X-RAY DIFFRACTION95
2.984-3.75520.22421690.17083177X-RAY DIFFRACTION97
3.7552-19.6850.23821940.17333238X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0142-0.2561-0.33380.4908-0.21640.9430.0383-0.3667-0.3285-0.05860.1234-0.0627-0.1295-0.0331-0.10380.06710.0218-0.06090.1370.08590.087429.40590.9171-10.265
20.2404-0.310.00220.33050.0080.0724-0.0504-0.03050.0376-0.0110.0062-0.08420.04360.0550.03970.0560.0242-0.00670.0950.02280.096618.06258.4331-20.2511
30.4748-0.2506-0.06231.7496-0.21880.1115-0.1059-0.1305-0.09980.14830.01660.03270.03320.06390.06170.04190.01910.02040.0202-0.0015-0.02315.972221.4459-19.8257
40.06590.0364-0.1310.0211-0.06950.28110.00790.0104-0.00010.0481-0.0040.0361-0.00240.013-0.00240.196-0.0233-0.01370.12230.02510.203425.53428.4299-18.5647
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 3:63)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 64:157)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 158:279)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 1)

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