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- PDB-4whh: A New Class of Peptidomimetics Targeting the Polo-box Domain of P... -

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Basic information

Entry
Database: PDB / ID: 4whh
TitleA New Class of Peptidomimetics Targeting the Polo-box Domain of Polo-like kinase 1
Components
  • C6H5(CH2)8-DERIVATIZED PEPTIDE INHIBITOR
  • Serine/threonine-protein kinase PLK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Polo-like kinase / inhibitor / peptide derivative / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / polo kinase / mitotic nuclear membrane disassembly / homologous chromosome segregation / protein localization to nuclear envelope / Phosphorylation of Emi1 ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / polo kinase / mitotic nuclear membrane disassembly / homologous chromosome segregation / protein localization to nuclear envelope / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / female meiosis chromosome segregation / nuclear membrane disassembly / synaptonemal complex / Phosphorylation of the APC/C / anaphase-promoting complex binding / Golgi inheritance / outer kinetochore / positive regulation of ubiquitin protein ligase activity / microtubule bundle formation / double-strand break repair via alternative nonhomologous end joining / mitotic chromosome condensation / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / regulation of mitotic spindle assembly / centrosome cycle / positive regulation of ubiquitin-protein transferase activity / regulation of mitotic metaphase/anaphase transition / sister chromatid cohesion / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / spindle midzone / mitotic G2 DNA damage checkpoint signaling / regulation of anaphase-promoting complex-dependent catabolic process / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / mitotic cytokinesis / positive regulation of proteolysis / negative regulation of double-strand break repair via homologous recombination / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cyclin A/B1/B2 associated events during G2/M transition / protein localization to chromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / centriole / 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 / regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / Condensation of Prophase Chromosomes / mitotic spindle organization / regulation of cytokinesis / establishment of protein localization / RHO GTPases Activate Formins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / protein destabilization / peptidyl-serine phosphorylation / kinetochore / positive regulation of protein localization to nucleus / centriolar satellite / G2/M transition of mitotic cell cycle / spindle / spindle pole / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / mitotic cell cycle / microtubule cytoskeleton / midbody / microtubule binding / protein phosphorylation / protein kinase activity / regulation of cell cycle / protein ubiquitination / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein kinase binding / negative regulation of apoptotic process / chromatin / magnesium ion binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
POLO box domain / Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / Arylsulfatase, C-terminal domain / POLO box domain / POLO box domain profile. / Serine/threonine-protein kinase, active site ...POLO box domain / Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / Arylsulfatase, C-terminal domain / POLO box domain / POLO box domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
C6H5(CH2)8-derivatized peptide inhibitor / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBang, J.K.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Korea Basic Science InstituteT34418 Korea, Republic Of
Rural Development AdministrationPJ009594 Korea, Republic Of
CitationJournal: J.Med.Chem. / Year: 2015
Title: A new class of peptidomimetics targeting the polo-box domain of polo-like kinase 1.
Authors: Ahn, M. / Han, Y.H. / Park, J.E. / Kim, S. / Lee, W.C. / Lee, S.J. / Gunasekaran, P. / Cheong, C. / Shin, S.Y. / Kim, H.Y. / Ryu, E.K. / Murugan, R.N. / Kim, N.H. / Bang, J.K.
History
DepositionSep 22, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 2.0Mar 27, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy
Category: citation / entity_poly ...citation / entity_poly / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_poly.type ..._citation.journal_id_CSD / _entity_poly.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
B: C6H5(CH2)8-DERIVATIZED PEPTIDE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2924
Polymers28,1002
Non-polymers1922
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-32 kcal/mol
Surface area10540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.927, 58.300, 66.753
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine/threonine-protein kinase PLK1 / Polo-like kinase 1 / PLK-1 / Serine/threonine-protein kinase 13 / STPK13


Mass: 27285.158 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 371-603
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53350, polo kinase
#2: Protein/peptide C6H5(CH2)8-DERIVATIZED PEPTIDE INHIBITOR


Type: Polypeptide / Class: Enzyme inhibitor / Mass: 814.842 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: C6H5(CH2)8-derivatized peptide inhibitor
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, 2.0M Ammonium sulfate

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 18067 / % possible obs: 97.6 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.069 / Χ2: 2.722 / Net I/av σ(I): 53.909 / Net I/σ(I): 15.1 / Num. measured all: 208591
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.9311.70.4349142.883100
1.93-1.9711.70.3549192.91100
1.97-2.0111.90.3128972.875100
2.01-2.0511.80.2158911.945100
2.05-2.0911.80.1999262.2100
2.09-2.1411.90.1998962.734100
2.14-2.1911.80.1669002.905100
2.19-2.2511.80.139322.435100
2.25-2.3211.80.1379132.88100
2.32-2.3911.90.1429143.323100
2.39-2.4811.80.1019062.355100
2.48-2.5811.80.0969252.452100
2.58-2.711.80.0929193.078100
2.7-2.8411.80.0699162.4100
2.84-3.0211.70.0599272.41399.7
3.02-3.2511.50.0579183.18798.5
3.25-3.5811.30.0449132.4597.2
3.58-4.0910.90.0448692.97991.9
4.09-5.1610.10.048053.04383.2
5.16-509.80.0438673.2183.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
ADSC2.5.6data collection
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RQ7

3rq7


Resolution: 1.9→43.91 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.2358 / WRfactor Rwork: 0.1901 / FOM work R set: 0.8576 / SU B: 3.053 / SU ML: 0.091 / SU R Cruickshank DPI: 0.1591 / SU Rfree: 0.1495 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 904 5 %RANDOM
Rwork0.1907 17119 --
obs0.1928 18067 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.64 Å2 / Biso mean: 32.986 Å2 / Biso min: 15.93 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å20 Å2
2---0.97 Å20 Å2
3---2.33 Å2
Refinement stepCycle: final / Resolution: 1.9→43.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1754 0 11 47 1812
Biso mean--49.55 34.27 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191800
X-RAY DIFFRACTIONr_bond_other_d0.0060.021693
X-RAY DIFFRACTIONr_angle_refined_deg1.9891.9952432
X-RAY DIFFRACTIONr_angle_other_deg1.363.0083892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0765209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93923.37580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64415310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4531512
X-RAY DIFFRACTIONr_chiral_restr0.110.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021968
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02425
X-RAY DIFFRACTIONr_mcbond_it2.9292.934848
X-RAY DIFFRACTIONr_mcbond_other2.932.935847
X-RAY DIFFRACTIONr_mcangle_it4.1014.3841053
LS refinement shellResolution: 1.895→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 66 -
Rwork0.201 1207 -
all-1273 -
obs--95.43 %

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