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- PDB-4qyh: CHK1 kinase domain in complex with diazacarbazole GNE-783 -

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Basic information

Entry
Database: PDB / ID: 4qyh
TitleCHK1 kinase domain in complex with diazacarbazole GNE-783
ComponentsSerine/threonine-protein kinase Chk1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / phosphotransfer catalyst / 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-3DX / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWiesmann, C. / Wu, P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2014
Title: Discovery of the 1,7-diazacarbazole class of inhibitors of checkpoint kinase 1.
Authors: Gazzard, L. / Appleton, B. / Chapman, K. / Chen, H. / Clark, K. / Drobnick, J. / Goodacre, S. / Halladay, J. / Lyssikatos, J. / Schmidt, S. / Sideris, S. / Wiesmann, C. / Williams, K. / Wu, ...Authors: Gazzard, L. / Appleton, B. / Chapman, K. / Chen, H. / Clark, K. / Drobnick, J. / Goodacre, S. / Halladay, J. / Lyssikatos, J. / Schmidt, S. / Sideris, S. / Wiesmann, C. / Williams, K. / Wu, P. / Yen, I. / Malek, S.
History
DepositionJul 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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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)69,1474
Polymers68,4102
Non-polymers7372
Water5,405300
1
A: Serine/threonine-protein kinase Chk1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5742
Polymers34,2051
Non-polymers3681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase Chk1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5742
Polymers34,2051
Non-polymers3681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.078, 65.962, 115.682
Angle α, β, γ (deg.)90.00, 94.49, 90.00
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: 34205.199 Da / Num. of mol.: 2 / Fragment: kinase domain, UNP residues 1-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHEK1, CHK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O14757, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-3DX / 3-[4-(4-methylpiperazin-1-yl)phenyl]-9H-pyrrolo[2,3-b:5,4-c']dipyridine-6-carbonitrile


Mass: 368.434 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H20N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 15% isopropanol, 12% PEG 8000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 5, 2007
RadiationMonochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 52841 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 21.6 Å2 / Rsym value: 0.071 / Net I/σ(I): 15.9

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Processing

Software
NameVersionClassification
BOSdata collection
AMoREphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.368 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23546 2689 5.1 %RANDOM
Rwork0.19731 ---
obs0.19931 50152 99.01 %-
all-52841 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.534 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20.17 Å2
2--0.18 Å20 Å2
3---0.74 Å2
Refine analyzeLuzzati coordinate error free: 0.139 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4288 0 56 300 4644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224454
X-RAY DIFFRACTIONr_bond_other_d0.0010.024044
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9826034
X-RAY DIFFRACTIONr_angle_other_deg0.81239434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5135524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82724.34212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26615790
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3891528
X-RAY DIFFRACTIONr_chiral_restr0.0810.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024856
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02880
X-RAY DIFFRACTIONr_nbd_refined0.1940.2839
X-RAY DIFFRACTIONr_nbd_other0.1740.24030
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22118
X-RAY DIFFRACTIONr_nbtor_other0.0810.22447
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.2117
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.223
X-RAY DIFFRACTIONr_mcbond_it3.5082.53449
X-RAY DIFFRACTIONr_mcbond_other0.6482.51062
X-RAY DIFFRACTIONr_mcangle_it4.05954264
X-RAY DIFFRACTIONr_scbond_it3.1892.52268
X-RAY DIFFRACTIONr_scangle_it4.44251770
LS refinement shellResolution: 1.9→1.94 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.318 161 -
Rwork0.272 2872 -
obs--96.87 %
Refinement TLS params.Method: refined / Origin x: -2.3622 Å / Origin y: -3.1905 Å / Origin z: 29.0968 Å
111213212223313233
T-0.0329 Å20.0097 Å20.0024 Å2--0.0249 Å2-0.0411 Å2---0.0168 Å2
L0.1645 °20.0847 °2-0.165 °2-0.2187 °2-0.4454 °2--0.9075 °2
S-0.0262 Å °0.068 Å °-0.0765 Å °-0.0181 Å °-0.008 Å °-0.0191 Å °0.0806 Å °0.015 Å °0.0342 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B401 - 604
2X-RAY DIFFRACTION1A401 - 496
3X-RAY DIFFRACTION1B301
4X-RAY DIFFRACTION1A301
5X-RAY DIFFRACTION1B3 - 273
6X-RAY DIFFRACTION1A3 - 273

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