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- PDB-2r0u: Crystal Structure of Chek1 in Complex with Inhibitor 54 -

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Basic information

Entry
Database: PDB / ID: 2r0u
TitleCrystal Structure of Chek1 in Complex with Inhibitor 54
ComponentsSerine/threonine-protein kinase Chk1
KeywordsTRANSFERASE / Chek1 / Kinase / cell cycle check point / ATP-binding / Cytoplasm / DNA damage / DNA repair / Nucleotide-binding / Nucleus / Phosphorylation / Polymorphism / Serine/threonine-protein kinase / Ubl conjugation
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-M54 / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsYan, Y. / Ikuta, M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Synthesis and evaluation of substituted benzoisoquinolinones as potent inhibitors of Chk1 kinase.
Authors: Garbaccio, R.M. / Huang, S. / Tasber, E.S. / Fraley, M.E. / Yan, Y. / Munshi, S. / Ikuta, M. / Kuo, L. / Kreatsoulas, C. / Stirdivant, S. / Drakas, B. / Rickert, K. / Walsh, E.S. / Hamilton, ...Authors: Garbaccio, R.M. / Huang, S. / Tasber, E.S. / Fraley, M.E. / Yan, Y. / Munshi, S. / Ikuta, M. / Kuo, L. / Kreatsoulas, C. / Stirdivant, S. / Drakas, B. / Rickert, K. / Walsh, E.S. / Hamilton, K.A. / Buser, C.A. / Hardwick, J. / Mao, X. / Beck, S.C. / Abrams, M.T. / Tao, W. / Lobell, R. / Sepp-Lorenzino, L. / Hartman, G.D.
History
DepositionAug 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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)37,3332
Polymers36,9221
Non-polymers4101
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.260, 65.540, 58.500
Angle α, β, γ (deg.)90.00, 94.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase Chk1


Mass: 36922.152 Da / Num. of mol.: 1 / Fragment: Protein kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRAD2030 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O14757, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-M54 / 6-(3-aminopropyl)-4-(3-hydroxyphenyl)-9-(1H-pyrazol-4-yl)benzo[h]isoquinolin-1(2H)-one


Mass: 410.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H22N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 13% PEG8K, 0.1M ammonium sulfate, 2% glycerol, 0.1M sodium cacodylate buffer, 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 IV++ / Detector: IMAGE PLATE / Date: Oct 27, 2005 / Details: blue Max-Flux confocal optical system
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→58 Å / Num. all: 26987 / Num. obs: 26669 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.91 % / Biso Wilson estimate: 30.747 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 15.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.85 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 4 / Num. unique all: 2675 / % possible all: 97.3

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Processing

Software
NameVersionClassification
BUSTER-TNT2.1.1refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1IA8

1ia8


Resolution: 1.9→58 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 1333 5 %RANDOM
Rwork0.1953 ---
obs0.1965 26662 98.65 %-
Displacement parametersBiso mean: 37.12 Å2
Baniso -1Baniso -2Baniso -3
1-2.36710594 Å20 Å20.09719814 Å2
2---2.18739559 Å20 Å2
3----0.17971035 Å2
Refinement stepCycle: LAST / Resolution: 1.9→58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2186 0 31 254 2471
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0122722
X-RAY DIFFRACTIONt_angle_deg1.12230592
X-RAY DIFFRACTIONt_dihedral_angle_d20.154770
X-RAY DIFFRACTIONt_trig_c_planes0.012722
X-RAY DIFFRACTIONt_gen_planes0.0163245
X-RAY DIFFRACTIONt_it1.669227220
X-RAY DIFFRACTIONt_nbd0.073285
LS refinement shellResolution: 1.9→2.01 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2588 194 4.64 %
Rwork0.2212 3990 -
all22.3 4184 -
obs--98.65 %

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