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- PDB-2xkd: Structure of Nek2 bound to aminopyrazine compound 12 -

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Basic information

Entry
Database: PDB / ID: 2xkd
TitleStructure of Nek2 bound to aminopyrazine compound 12
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 / protein autophosphorylation / midbody / protein phosphatase binding / microtubule / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / 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 / cytoplasm / cytosol
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-T3M / Serine/threonine-protein kinase Nek2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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)33,1505
Polymers32,6621
Non-polymers4884
Water2,828157
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.280, 57.060, 73.760
Angle α, β, γ (deg.)90.00, 127.61, 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-T3M / 4-[3-amino-6-(3,4,5-trimethoxyphenyl)pyrazin-2-yl]benzoic acid


Mass: 381.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19N3O5
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.56 Å3/Da / Density % sol: 51.94 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.96→49.95 Å / Num. obs: 21360 / % possible obs: 89.6 % / Observed criterion σ(I): 6 / Redundancy: 3.5 % / Biso Wilson estimate: 24.13 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.2
Reflection shellResolution: 1.96→2.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 4.4 / % possible all: 98.2

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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: 1.96→31.289 Å / SU ML: 0.2 / σ(F): 0.03 / Phase error: 20.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2169 1031 5.1 %
Rwork0.1809 --
obs0.1828 20398 85.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.755 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.8701 Å20 Å23.8189 Å2
2---5.4822 Å20 Å2
3---10.3523 Å2
Refinement stepCycle: LAST / Resolution: 1.96→31.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2015 0 31 157 2203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062097
X-RAY DIFFRACTIONf_angle_d0.9832833
X-RAY DIFFRACTIONf_dihedral_angle_d18.37785
X-RAY DIFFRACTIONf_chiral_restr0.067309
X-RAY DIFFRACTIONf_plane_restr0.005360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.06340.23541560.17742890X-RAY DIFFRACTION90
2.0634-2.19260.20121250.17072570X-RAY DIFFRACTION80
2.1926-2.36180.2141020.19022069X-RAY DIFFRACTION64
2.3618-2.59940.21011730.17463200X-RAY DIFFRACTION99
2.5994-2.97530.23341530.17872780X-RAY DIFFRACTION86
2.9753-3.74760.20681550.17582810X-RAY DIFFRACTION87
3.7476-31.29310.19971670.17843048X-RAY DIFFRACTION92
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)
11.6186-0.4107-1.11340.7593-0.62192.1005-0.0260.50620.3834-0.1249-0.1045-0.34760.2364-0.17330.11170.1933-0.0240.0380.27240.07880.209129.0051-0.66369.7474
21.46760.53560.16290.5643-0.03710.4035-0.07120.10170.05-0.01150.0411-0.0488-0.01820.13790.04030.1067-0.0168-0.00060.14630.00640.123317.9254-7.965219.9185
30.56780.26870.08041.5728-0.2420.5575-0.08090.10160.0219-0.09490.08580.05120.08420.0461-0.00820.1231-0.0243-0.00870.1148-0.00170.09436.1158-21.060418.9292
42.0894-0.20371.42540.50821.50629.0086-0.06150.0378-0.4832-0.14650.2565-0.1540.824-0.0019-0.15080.2236-0.0432-0.00170.14850.01570.3125.5896-8.67618.8651
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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