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- PDB-7bko: Crystal structure of CHK1 complex with compound 9 -

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Basic information

Entry
Database: PDB / ID: 7bko
TitleCrystal structure of CHK1 complex with compound 9
ComponentsSerine/threonine-protein kinase Chk1
KeywordsTRANSFERASE / PARKINSON'S DISEASE / LEUCINE-RICH REPEAT KINASE 2 / LRRK2 / CHECKPOINT KINASE 1 / CHK1 / MUTANT / SURROGATE / KINASE INHIBITOR / SBDD
Function / homology
Function and homology information


negative regulation of G0 to G1 transition / apoptotic process involved in development / negative regulation of DNA biosynthetic process / regulation of mitotic centrosome separation / negative regulation of mitotic nuclear division / mitotic G2/M transition checkpoint / inner cell mass cell proliferation / regulation of double-strand break repair via homologous recombination / negative regulation of gene expression, epigenetic / nucleus organization ...negative regulation of G0 to G1 transition / apoptotic process involved in development / negative regulation of DNA biosynthetic process / regulation of mitotic centrosome separation / negative regulation of mitotic nuclear division / mitotic G2/M transition checkpoint / 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 / mitotic G2 DNA damage checkpoint signaling / Transcriptional Regulation by E2F6 / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / signal transduction in response to DNA damage / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Activation of ATR in response to replication stress / positive regulation of cell cycle / peptidyl-threonine phosphorylation / DNA damage checkpoint signaling / condensed nuclear chromosome / regulation of signal transduction by p53 class mediator / replication fork / TP53 Regulates Transcription of DNA Repair Genes / 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 / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / DNA replication / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / chromatin remodeling / protein domain specific binding / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / intracellular membrane-bounded organelle / apoptotic process / centrosome / DNA damage response / chromatin / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Checkpoint kinase 1, catalytic domain / 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
Similarity search - Domain/homology
1H-pyrazolo[3,4-d]pyrimidin-4-amine / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBaker, L.M. / Surgenor, A.E. / Williamson, D.S.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Design and Synthesis of Pyrrolo[2,3- d ]pyrimidine-Derived Leucine-Rich Repeat Kinase 2 (LRRK2) Inhibitors Using a Checkpoint Kinase 1 (CHK1)-Derived Crystallographic Surrogate.
Authors: Williamson, D.S. / Smith, G.P. / Mikkelsen, G.K. / Jensen, T. / Acheson-Dossang, P. / Badolo, L. / Bedford, S.T. / Chell, V. / Chen, I.J. / Dokurno, P. / Hentzer, M. / Newland, S. / Ray, S.C. ...Authors: Williamson, D.S. / Smith, G.P. / Mikkelsen, G.K. / Jensen, T. / Acheson-Dossang, P. / Badolo, L. / Bedford, S.T. / Chell, V. / Chen, I.J. / Dokurno, P. / Hentzer, M. / Newland, S. / Ray, S.C. / Shaw, T. / Surgenor, A.E. / Terry, L. / Wang, Y. / Christensen, K.V.
History
DepositionJan 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)34,2832
Polymers34,1481
Non-polymers1351
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.011, 65.761, 58.102
Angle α, β, γ (deg.)90.000, 94.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase Chk1 / CHK1 checkpoint homolog / Cell cycle checkpoint kinase / Checkpoint kinase-1


Mass: 34148.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHEK1, CHK1 / Plasmid: Pfastbac1 / Details (production host): CHK1 1-289 C8H / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O14757, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-TVW / 1H-pyrazolo[3,4-d]pyrimidin-4-amine / 2~{H}-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10-30% PEG8K 0.1M HEPES pH 7.5 15% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→26.54 Å / Num. obs: 26484 / % possible obs: 89.7 % / Redundancy: 1.58 % / Rmerge(I) obs: 0.125 / Rrim(I) all: 0.125 / Χ2: 3.11 / Net I/σ(I): 4.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsΧ2% possible allRejects
2.3-2.381.520.4061.5408626901.6190.6
2.38-2.481.520.391.6410926961.5991.6
2.48-2.591.540.3641.8411726801.8891.5
2.59-2.731.550.3242.1422027222.1291.52
2.73-2.91.560.2792.4419026772.2491.46
2.9-3.121.580.2263.2429227042.4991.77
3.12-3.431.60.1874434327063.3890.919
3.43-3.931.60.1226.6423626074.8489.165
3.93-4.951.620.0819.5429825885.0187.1100
4.95-26.521.740.07310.3436024145.1582.1166

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Processing

Software
NameVersionClassification
d*TREKdata reduction
d*TREK7.1SSIdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IA8

1ia8


Resolution: 2.3→26.54 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.864 / SU B: 15.708 / SU ML: 0.354 / SU R Cruickshank DPI: 0.4216 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.422 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3307 732 5.1 %RANDOM
Rwork0.2415 ---
obs0.2461 13621 94.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.73 Å2 / Biso mean: 51.648 Å2 / Biso min: 13.51 Å2
Baniso -1Baniso -2Baniso -3
1--2.63 Å20 Å2-0.94 Å2
2---0.09 Å20 Å2
3---2.83 Å2
Refinement stepCycle: final / Resolution: 2.3→26.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 10 212 2323
Biso mean--59.31 45.03 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132161
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172063
X-RAY DIFFRACTIONr_angle_refined_deg1.791.6422925
X-RAY DIFFRACTIONr_angle_other_deg1.3751.5854756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5575257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61922.627118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.15315387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9291514
X-RAY DIFFRACTIONr_chiral_restr0.0910.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022409
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02488
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 52 -
Rwork0.366 1035 -
all-1087 -
obs--95.86 %

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