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- PDB-7bk1: Crystal structure of CHK1-10pt-mutant complex with compound 32 -

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Basic information

Entry
Database: PDB / ID: 7bk1
TitleCrystal structure of CHK1-10pt-mutant complex with compound 32
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 / histone H3T11 kinase activity / 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 / nucleus organization / negative regulation of gene expression, epigenetic ...negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / 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 / nucleus organization / negative regulation of gene expression, epigenetic / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / peptidyl-threonine phosphorylation / 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 / DNA damage checkpoint signaling / regulation of signal transduction by p53 class mediator / replication fork / condensed nuclear chromosome / TP53 Regulates Transcription of DNA Repair Genes / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / cellular response to mechanical stimulus / Signaling by SCF-KIT / G2/M DNA damage checkpoint / 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 / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / protein domain specific binding / protein serine kinase activity / DNA repair / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / apoptotic process / DNA damage response / centrosome / chromatin / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
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
Chem-U0N / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDokurno, P. / 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 15, 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)34,5314
Polymers34,0941
Non-polymers4363
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-14 kcal/mol
Surface area12530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.894, 65.752, 54.975
Angle α, β, γ (deg.)90.000, 99.880, 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: 34094.207 Da / Num. of mol.: 1
Mutation: N59L, V68I, L84M, Y86L, C87A, E91S, E134H, S147A, F149Y, G150S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHEK1, CHK1 / Plasmid: Pfastbac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O14757, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-U0N / 4-amino-2-[(1,3-dimethyl-1H-pyrazol-4-yl)amino]-7-methyl-6-[(2R)-2-methylpyrrolidin-1-yl]-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile / 4-azanyl-2-[(1,3-dimethylpyrazol-4-yl)amino]-7-methyl-6-[(2~{R})-2-methylpyrrolidin-1-yl]pyrrolo[2,3-d]pyrimidine-5-carbonitrile


Mass: 365.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H23N9 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 7% PEG 8000, 0.1 M MES buffer pH 6.5, 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.5418 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Oct 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→22.3 Å / Num. obs: 21388 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.1 Å / Redundancy: 3 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2892 / % possible all: 99.3

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Processing

Software
NameVersionClassification
SAINTdata reduction
SAINTdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5oop

5oop


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.758 / SU ML: 0.124 / SU R Cruickshank DPI: 0.1743 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 1030 4.8 %RANDOM
Rwork0.1899 ---
obs0.192 20337 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.87 Å2 / Biso mean: 33.568 Å2 / Biso min: 12.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å2-0 Å20.15 Å2
2---0.05 Å2-0 Å2
3---1.31 Å2
Refinement stepCycle: final / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 29 205 2281
Biso mean--40.63 39.28 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132127
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171966
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.6452894
X-RAY DIFFRACTIONr_angle_other_deg1.3971.5764554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3655255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.34622.752109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01915356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5351512
X-RAY DIFFRACTIONr_chiral_restr0.0850.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022353
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02430
LS refinement shellResolution: 2→2.107 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.297 153 -
Rwork0.285 2910 -
obs--99.32 %

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