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- PDB-3tki: Crystal structure of Chk1 in complex with inhibitor S25 -

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Basic information

Entry
Database: PDB / ID: 3tki
TitleCrystal structure of Chk1 in complex with inhibitor S25
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 / nucleus organization ...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 / nucleus organization / negative regulation of gene expression, epigenetic / 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 / positive regulation of cell cycle / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Activation of ATR in response to replication stress / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / condensed nuclear chromosome / replication fork / TP53 Regulates Transcription of DNA Repair Genes / peptidyl-threonine phosphorylation / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Signaling by SCF-KIT / G2/M DNA damage checkpoint / cellular response to mechanical stimulus / G2/M transition of mitotic cell cycle / regulation of cell population proliferation / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / DNA replication / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / protein phosphorylation / protein domain specific binding / intracellular membrane-bounded organelle / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / DNA damage response / chromatin / apoptotic process / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
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-S25 / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 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)37,4443
Polymers36,9221
Non-polymers5222
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.000, 65.240, 57.910
Angle α, β, γ (deg.)90.00, 94.53, 90.00
Int Tables number4
Space group name H-MP1211
Detailsone monomer per symmetric 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-S25 / N-(2-aminoethyl)-5-(2-{[4-(morpholin-4-yl)pyridin-2-yl]amino}-1,3-thiazol-5-yl)pyridine-3-carboxamide


Mass: 425.507 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N7O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 46.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 13% PEG8K, 0.1M amminium 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: Feb 9, 2005 / 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: 1.6→57.73 Å / Num. all: 44122 / Num. obs: 41034 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.63 % / Biso Wilson estimate: 27.37 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 19.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.04 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 3 / Num. unique all: 2472 / Rsym value: 0.359 / % possible all: 57.2

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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: 1.6→23.43 Å / Cor.coef. Fo:Fc: 0.9604 / Cor.coef. Fo:Fc free: 0.9499 / SU R Cruickshank DPI: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2119 2054 5.01 %RANDOM
Rwork0.1863 ---
obs0.1876 41010 92.97 %-
all-44122 --
Displacement parametersBiso mean: 33.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.5719 Å20 Å20.0689 Å2
2---2.7248 Å20 Å2
3---1.1529 Å2
Refine analyzeLuzzati coordinate error obs: 0.193 Å
Refinement stepCycle: LAST / Resolution: 1.6→23.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2176 0 35 222 2433
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012266HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.013073HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d784SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes326HARMONIC5
X-RAY DIFFRACTIONt_it2266HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion17.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion282SEMIHARMONIC5
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_contact2835SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 100 5.72 %
Rwork0.2622 1649 -
all0.2639 1749 -
obs--92.97 %

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