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- PDB-3dbd: Crystal structure of an activated (Thr->Asp) Polo-like kinase 1 (... -

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Basic information

Entry
Database: PDB / ID: 3dbd
TitleCrystal structure of an activated (Thr->Asp) Polo-like kinase 1 (Plk1) catalytic domain in complex with Compound 094
ComponentsPolo-like kinase 1
KeywordsTRANSFERASE / Polo-like kinase 1 / Plk1 / catalytic domain / small-molecule inhibitor / Kinase
Function / homology
Function and homology information


Phosphorylation of Emi1 / Condensation of Prophase Chromosomes / Resolution of Sister Chromatid Cohesion / Regulation of PLK1 Activity at G2/M Transition / Mitotic Metaphase/Anaphase Transition / Mitotic Telophase/Cytokinesis / EML4 and NUDC in mitotic spindle formation / Polo-like kinase mediated events / Cyclin A/B1/B2 associated events during G2/M transition / The role of GTSE1 in G2/M progression after G2 checkpoint ...Phosphorylation of Emi1 / Condensation of Prophase Chromosomes / Resolution of Sister Chromatid Cohesion / Regulation of PLK1 Activity at G2/M Transition / Mitotic Metaphase/Anaphase Transition / Mitotic Telophase/Cytokinesis / EML4 and NUDC in mitotic spindle formation / Polo-like kinase mediated events / Cyclin A/B1/B2 associated events during G2/M transition / The role of GTSE1 in G2/M progression after G2 checkpoint / polo kinase / mitotic spindle organization / kinetochore / spindle pole / mitotic cell cycle / retina development in camera-type eye / midbody / cell division / protein serine/threonine kinase activity / centrosome / ATP binding / nucleus / cytoplasm
Similarity search - Function
Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 ...Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box 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, ATP binding site / Protein kinases ATP-binding region signature. / 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-3FR / Serine/threonine-protein kinase PLK
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsElling, R.A. / Barr, K.J. / Romanowski, M.J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Design and synthesis of 2-amino-pyrazolopyridines as Polo-like kinase 1 inhibitors.
Authors: Fucini, R.V. / Hanan, E.J. / Romanowski, M.J. / Elling, R.A. / Lew, W. / Barr, K.J. / Zhu, J. / Yoburn, J.C. / Liu, Y. / Fahr, B.T. / Fan, J. / Lu, Y. / Pham, P. / Choong, I.C. / ...Authors: Fucini, R.V. / Hanan, E.J. / Romanowski, M.J. / Elling, R.A. / Lew, W. / Barr, K.J. / Zhu, J. / Yoburn, J.C. / Liu, Y. / Fahr, B.T. / Fan, J. / Lu, Y. / Pham, P. / Choong, I.C. / VanderPorten, E.C. / Bui, M. / Purkey, H.E. / Evanchik, M.J. / Yang, W.
History
DepositionMay 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polo-like kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4752
Polymers35,9931
Non-polymers4821
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.267, 135.267, 135.267
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Polo-like kinase 1


Mass: 35992.953 Da / Num. of mol.: 1 / Fragment: Plk1 kinase domain / Mutation: T196D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: plk1 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star Codon+ / References: UniProt: Q4KMI8, polo kinase
#2: Chemical ChemComp-3FR / 3'-chloro-5'-(3-methyl-6-{[(1S)-1-phenylethyl]amino}-1H-pyrazolo[4,3-c]pyridin-1-yl)biphenyl-2-carboxamide / 3'-chloro-5'-[3-methyl-6-(1-phenyl-ethylamino)-pyrazolo[4,3-c]pyridin-1-yl]-biphenyl-2-carboxylic acid amide


Mass: 481.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H24ClN5O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.87 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: hanging-drop vapor diffusion at 4 C (277K); protein at 7 mg/ml in 50 mM Tris-HCl pH 7.5, 200 mM NaCl and 3 mM DTT; crystallization condition: 0.1 M tri-sodium citrate pH 5.6, 0.2 M (NH4) ...Details: hanging-drop vapor diffusion at 4 C (277K); protein at 7 mg/ml in 50 mM Tris-HCl pH 7.5, 200 mM NaCl and 3 mM DTT; crystallization condition: 0.1 M tri-sodium citrate pH 5.6, 0.2 M (NH4)2SO4, and 25% PEG 3350; cryoprotectant: 15% ethylene glycol., VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2007
RadiationMonochromator: Side-scattering cube root I-beam bent single crystal; asymmetric cut 12.2 degs. Crystal type: Si(311)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.05→30 Å / Num. obs: 7979 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.5
Reflection shellResolution: 3.05→3.21 Å / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3d5w

3d5w


Resolution: 3.05→30 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.871 / SU B: 22.309 / SU ML: 0.385 / Cross valid method: THROUGHOUT / ESU R Free: 0.472 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27565 778 9.8 %RANDOM
Rwork0.24969 ---
obs0.25233 7201 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.728 Å2
Refinement stepCycle: LAST / Resolution: 3.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2081 0 35 2 2118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222168
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0051.9952935
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8755259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.06722.79693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06515378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1321517
X-RAY DIFFRACTIONr_chiral_restr0.0490.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.021631
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1580.2943
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.21504
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0670.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7282.51339
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32152120
X-RAY DIFFRACTIONr_scbond_it0.242.5948
X-RAY DIFFRACTIONr_scangle_it0.4345815
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.05→3.157 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.401 76 -
Rwork0.337 700 -
obs--100 %

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