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- PDB-2e9v: Structure of h-CHK1 complexed with A859017 -

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Basic information

Entry
Database: PDB / ID: 2e9v
TitleStructure of h-CHK1 complexed with A859017
ComponentsSerine/threonine-protein kinase Chk1
KeywordsTRANSFERASE / Protein-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-85A / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPark, C.
CitationJournal: To be Published
Title: Structure-Based Design, Synthesis and Biological Evaluation of Potent Selective Macrocyclic Chk1 Inhibitors
Authors: Tong, Y. / Claiborne, A. / Stewart, K.D. / Park, C. / Kovar, P. / Chen, Z. / Credo, R.B. / Gwaltney, S.L. / Zhang, H. / Rosenberg, S.H. / Sham, H.L. / Sowin, T.J. / Lin, N.H.
History
DepositionJan 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 28, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Serine/threonine-protein kinase Chk1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8394
Polymers61,8792
Non-polymers9602
Water7,746430
1
A: Serine/threonine-protein kinase Chk1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4192
Polymers30,9401
Non-polymers4801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-4 kcal/mol
Surface area13690 Å2
MethodPISA
2
B: Serine/threonine-protein kinase Chk1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4192
Polymers30,9401
Non-polymers4801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-4 kcal/mol
Surface area13730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.883, 56.783, 64.595
Angle α, β, γ (deg.)92.83, 104.39, 113.86
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Serine/threonine-protein kinase Chk1


Mass: 30939.562 Da / Num. of mol.: 2 / Fragment: residues 2-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: O14757, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-85A / 18-CHLORO-2-OXO-17-[(PYRIDIN-4-YLMETHYL)AMINO]-2,3,11,12,13,14-HEXAHYDRO-1H,10H-4,8-(AZENO)-9,15,1,3,6-BENZODIOXATRIAZACYCLOHEPTADECINE-7-CARBONITRILE / 7-CHLORO-3-OXO-8-[(PYRIDIN-4-YLMETHYL)-AMINO]-11,17-DIOXA-2,4,20,22-TETRAAZA-TRICYCLO[16.3.1.0*5,10*]DOCOSA-1(21),5(10)6,8,18(22),19-HEXAENE-19-CARBONITRILE


Mass: 479.919 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H22ClN7O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 8000, isopropanol, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Nov 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 38402 / Num. obs: 32755 / % possible obs: 85.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Biso Wilson estimate: 34.5 Å2 / Rsym value: 0.06 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2870 / Rsym value: 0.245 / % possible all: 36.1

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Processing

Software
NameVersionClassification
CNX2002refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 582152.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.333 2783 10 %RANDOM
Rwork0.257 ---
all0.279 38402 --
obs0.272 27793 72.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 90.7279 Å2 / ksol: 0.447384 e/Å3
Displacement parametersBiso mean: 45.7 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å2-5.07 Å22.24 Å2
2---11.99 Å2-8.95 Å2
3---10.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.29 Å
Luzzati d res low-6 Å
Luzzati sigma a0.24 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4352 0 68 430 4850
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it0.751.5
X-RAY DIFFRACTIONc_mcangle_it1.32
X-RAY DIFFRACTIONc_scbond_it0.842
X-RAY DIFFRACTIONc_scangle_it1.272.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.328 124 9 %
Rwork0.302 1255 -
obs-1255 36.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.parmprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4a85.parama85.top

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