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- PDB-3tkh: Crystal structure of Chk1 in complex with inhibitor S01 -

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Basic information

Entry
Database: PDB / ID: 3tkh
TitleCrystal structure of Chk1 in complex with inhibitor S01
ComponentsSerine/threonine-protein kinase Chk1
Keywordstransferase/transferase inhibitor / chk1 / kinase / cell checkpoint / transferase-transferase inhibitor complex
Function / homology
Function and homology information


negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / mitotic G2/M transition checkpoint / negative regulation of mitotic nuclear division / regulation of mitotic centrosome separation / inner cell mass cell proliferation / regulation of double-strand break repair via homologous recombination / negative regulation of gene expression, epigenetic ...negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / mitotic G2/M transition checkpoint / negative regulation of mitotic nuclear division / regulation of mitotic centrosome separation / inner cell mass cell proliferation / regulation of double-strand break repair via homologous recombination / negative regulation of gene expression, epigenetic / nucleus organization / cellular response to caffeine / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / signal transduction in response to DNA damage / Activation of ATR in response to replication stress / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of cell cycle / regulation of signal transduction by p53 class mediator / condensed nuclear chromosome / replication fork / DNA damage checkpoint signaling / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / TP53 Regulates Transcription of DNA Repair Genes / peptidyl-threonine phosphorylation / G2/M DNA damage checkpoint / Signaling by SCF-KIT / cellular response to mechanical stimulus / G2/M transition of mitotic cell cycle / regulation of cell population proliferation / Processing of DNA double-strand break ends / DNA replication / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / protein domain specific binding / protein phosphorylation / intracellular membrane-bounded organelle / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / DNA damage response / chromatin / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Checkpoint kinase 1, catalytic domain / 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, ATP binding site ...Checkpoint kinase 1, catalytic domain / 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, 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-07S / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.79 Å
AuthorsYan, Y. / Ikuta, M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: Pyridyl aminothiazoles as potent inhibitors of Chk1 with slow dissociation rates.
Authors: Dudkin, V.Y. / Rickert, K. / Kreatsoulas, C. / Wang, C. / Arrington, K.L. / Fraley, M.E. / Hartman, G.D. / Yan, Y. / Ikuta, M. / Stirdivant, S.M. / Drakas, R.A. / Walsh, E.S. / Hamilton, K. ...Authors: Dudkin, V.Y. / Rickert, K. / Kreatsoulas, C. / Wang, C. / Arrington, K.L. / Fraley, M.E. / Hartman, G.D. / Yan, Y. / Ikuta, M. / Stirdivant, S.M. / Drakas, R.A. / Walsh, E.S. / Hamilton, K. / Buser, C.A. / Lobell, R.B. / Sepp-Lorenzino, L.
History
DepositionAug 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase Chk1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4843
Polymers36,9221
Non-polymers5622
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.091, 65.413, 57.821
Angle α, β, γ (deg.)90.00, 94.80, 90.00
Int Tables number4
Space group name H-MP1211
Detailsone monomer per asymmetric unit

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Components

#1: Protein Serine/threonine-protein kinase Chk1


Mass: 36922.152 Da / Num. of mol.: 1 / Fragment: chk1 kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHEK1, CHK1 / Plasmid: pRAD2030 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O14757, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-07S / 1-(morpholin-4-yl)-2-[4-(2-{[5-(pyridin-3-yl)-1,3-thiazol-2-yl]amino}pyridin-4-yl)piperazin-1-yl]ethanone


Mass: 465.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N7O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 13% PEG8K, 0.1M ammonium sulfate, 2% glycerol, 0.1M cacodylate buffer at pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Aug 27, 2004 / Details: blue confocal optical system
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.79→44.92 Å / Num. all: 31362 / Num. obs: 31331 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.79 % / Biso Wilson estimate: 28.15 Å2 / Rsym value: 0.063 / Net I/σ(I): 15.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.65 % / Mean I/σ(I) obs: 3 / Num. unique all: 3096 / Rsym value: 0.306 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CNSrefinement
BUSTER2.9.7refinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1IA8

1ia8


Resolution: 1.79→44.92 Å / Cor.coef. Fo:Fc: 0.9562 / Cor.coef. Fo:Fc free: 0.9556 / SU R Cruickshank DPI: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 1580 5.04 %RANDOM
Rwork0.1832 ---
obs0.1841 31330 98.88 %-
all-31362 --
Displacement parametersBiso mean: 32.57 Å2
Baniso -1Baniso -2Baniso -3
1-1.1786 Å20 Å2-0.3866 Å2
2---1.9623 Å20 Å2
3---0.7837 Å2
Refine analyzeLuzzati coordinate error obs: 0.195 Å
Refinement stepCycle: LAST / Resolution: 1.79→44.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 38 216 2390
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012228HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.013025HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d762SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes57HARMONIC2
X-RAY DIFFRACTIONt_gen_planes322HARMONIC5
X-RAY DIFFRACTIONt_it2228HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion17.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion278SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2769SEMIHARMONIC4
LS refinement shellResolution: 1.79→1.85 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2362 131 5.04 %
Rwork0.2282 2468 -
all0.2286 2599 -
obs--98.88 %

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