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- PDB-3be9: Structure-based design and synthesis of novel macrocyclic pyrazol... -

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Basic information

Entry
Database: PDB / ID: 3be9
TitleStructure-based design and synthesis of novel macrocyclic pyrazolo[1,5-a] [1,3,5]triazine compounds as potent inhibitors of protein kinase CK2 and their anticancer activities
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / STRUCTURE-BASED DRUG DESIGN / ENZYME-INHIBITOR COMPLEX / CASEIN KINASE II / PROTEIN KINASE CK2 / ATP-binding / Nucleotide-binding / Serine/threonine-protein kinase
Function / homology
Function and homology information


regulation of transcription by RNA polymerase I / regulation of transcription by RNA polymerase III / protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ATP binding ...regulation of transcription by RNA polymerase I / regulation of transcription by RNA polymerase III / protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ATP binding / nucleus / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / 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 ...Casein Kinase 2, subunit alpha / 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-P04 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsNie, Z. / Perretta, C. / Erickson, P. / Margosiak, S. / Lu, J. / Averill, A. / Almassy, R. / Chu, S.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Structure-based design and synthesis of novel macrocyclic pyrazolo[1,5-a] [1,3,5]triazine compounds as potent inhibitors of protein kinase CK2 and their anticancer activities.
Authors: Nie, Z. / Perretta, C. / Erickson, P. / Margosiak, S. / Lu, J. / Averill, A. / Almassy, R. / Chu, S.
History
DepositionNov 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8142
Polymers41,4501
Non-polymers3631
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.327, 59.578, 44.835
Angle α, β, γ (deg.)90.0, 103.419, 90.0
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-734-

HOH

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Components

#1: Protein Casein kinase II subunit alpha / CK II / CK2-alpha


Mass: 41450.465 Da / Num. of mol.: 1 / Mutation: V256A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ACK2 / Plasmid: PET-28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P28523, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-P04 / 19-(cyclopropylamino)-4,6,7,15-tetrahydro-5H-16,1-(azenometheno)-10,14-(metheno)pyrazolo[4,3-o][1,3,9]triazacyclohexadecin-8(9H)-one


Mass: 363.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N7O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14% PEG 4000, 0.05M Sodium Acetate, 0.10M TRISHCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 112 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54178
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 21, 2005 / Details: MIRRORS
RadiationMonochromator: OSMIC CONFOCAL MAX-FLUX MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→32.7 Å / Num. obs: 23749 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.54 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 16.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.5 / % possible all: 92

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Processing

Software
NameClassification
MAR345dtbdata collection
CNXrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2PVJ

2pvj


Resolution: 2→32.7 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2284 -RANDOM
Rwork0.19 ---
all-23749 --
obs-22890 91.6 %-
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.09 Å20 Å21.683 Å2
2---3.12 Å20 Å2
3----1.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 27 246 3007
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.91
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.96
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.882
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.334 191 -
Rwork0.269 1770 -
obs--78.4 %

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