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- PDB-4qyf: CHK1 kinase domain in complex with aminopyrazine compound 13 -

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Basic information

Entry
Database: PDB / ID: 4qyf
TitleCHK1 kinase domain in complex with aminopyrazine compound 13
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 / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-3DV / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsAppleton, B. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5132
Polymers34,2051
Non-polymers3071
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.971, 65.948, 58.118
Angle α, β, γ (deg.)90.00, 93.96, 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.: 1 / 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-3DV / 4-[3-amino-6-(3-hydroxyphenyl)pyrazin-2-yl]benzoic acid


Mass: 307.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 51.06 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 18, 2007
RadiationMonochromator: Varixmax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 18224 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 22.9 Å2 / Rsym value: 0.122 / Net I/σ(I): 13.6

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Processing

Software
NameVersionClassification
StructureStudiodata collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→15.858 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.122 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 950 5.2 %RANDOM
Rwork0.168 ---
obs0.171 17274 98.4 %-
all-18224 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-0.03 Å2
2--0.64 Å20 Å2
3----0.21 Å2
Refine analyzeLuzzati coordinate error free: 0.18 Å
Refinement stepCycle: LAST / Resolution: 2.15→15.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 23 194 2399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222258
X-RAY DIFFRACTIONr_bond_other_d0.0020.021569
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9773056
X-RAY DIFFRACTIONr_angle_other_deg0.90733818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9385266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1824.206107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74615401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8281515
X-RAY DIFFRACTIONr_chiral_restr0.0780.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022466
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
X-RAY DIFFRACTIONr_nbd_refined0.1870.2406
X-RAY DIFFRACTIONr_nbd_other0.1860.21597
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21076
X-RAY DIFFRACTIONr_nbtor_other0.0830.21101
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2153
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2910.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7352.51760
X-RAY DIFFRACTIONr_mcbond_other0.72.5537
X-RAY DIFFRACTIONr_mcangle_it4.29752173
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2632.51101
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4175883
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.19 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.289 49 -
Rwork0.2 966 -
obs--96.21 %
Refinement TLS params.Method: refined / Origin x: 5.1001 Å / Origin y: 12.1525 Å / Origin z: 6.507 Å
111213212223313233
T-0.0093 Å2-0.0011 Å20.0022 Å2--0.0185 Å2-0.0018 Å2---0.0087 Å2
L0.3046 °2-0.0726 °2-0.0776 °2-0.2147 °20.0544 °2--0.3717 °2
S-0.0166 Å °-0.001 Å °-0.0095 Å °0.0369 Å °0.0001 Å °0.0176 Å °0.0313 Å °0.0309 Å °0.0164 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 87
2X-RAY DIFFRACTION1A88 - 273
3X-RAY DIFFRACTION1A276 - 280

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