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- PDB-2pvh: Structure-Based Design of Pyrazolo[1,5-a][1,3,5]triazine Derivati... -

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Basic information

Entry
Database: PDB / ID: 2pvh
TitleStructure-Based Design of Pyrazolo[1,5-a][1,3,5]triazine Derivatives as Potent Inhibitors of Protein Kinase CK2
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Structure-Based Drug Design / Enzyme-Inhibitor Complex / Casein Kinase II / Protein Kinase CK2
Function / homology
Function and homology information


protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ATP binding / nucleus / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / 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 ...Casein Kinase 2, subunit alpha / 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-P19 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsNie, Z. / Perretta, C. / Erickson, P. / Margosiak, S. / Almassy, R. / Lu, J. / Averill, A. / Yager, K.M. / Chu, S.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Structure-based design, synthesis, and study of pyrazolo[1,5-a][1,3,5]triazine derivatives as potent inhibitors of protein kinase CK2.
Authors: Nie, Z. / Perretta, C. / Erickson, P. / Margosiak, S. / Almassy, R. / Lu, J. / Averill, A. / Yager, K.M. / Chu, S.
History
DepositionMay 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7532
Polymers41,4501
Non-polymers3021
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.294, 59.274, 44.943
Angle α, β, γ (deg.)90.00, 102.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-659-

HOH

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Components

#1: Protein Casein kinase II subunit alpha / CK II / CK2-alpha / Protein kinase 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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P28523, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-P19 / N,N'-DIPHENYLPYRAZOLO[1,5-A][1,3,5]TRIAZINE-2,4-DIAMINE


Mass: 302.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18% PEG 4000, 0.20M Sodium Acetate, 0.10M TrisHCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 107 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 10, 2005 / Details: MIRRORS
RadiationMonochromator: OSMIC CONFOCAL MAX-FLUX MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 18543 / Num. obs: 18543 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.059 / Χ2: 0.956 / Net I/σ(I): 21.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1796 / Χ2: 1.075 / % possible all: 97.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
DENZOdata reduction
CNXphasing
CNXrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1OM1 PROTEIN MODEL

1om1


Resolution: 2.2→50 Å / FOM work R set: 0.847 / Isotropic thermal model: ISOTROPIC / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1767 -RANDOM
Rwork0.192 ---
all0.196 18005 --
obs0.196 18005 100 %-
Displacement parametersBiso mean: 32.24 Å2
Baniso -1Baniso -2Baniso -3
1-8.933 Å20 Å22.149 Å2
2---11.559 Å20 Å2
3---2.627 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.321 Å0.249 Å
Luzzati d res low-5 Å
Luzzati sigma a0.303 Å0.226 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 23 161 2918
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0056
X-RAY DIFFRACTIONc_angle_deg1.16
X-RAY DIFFRACTIONc_dihedral_angle_d20.91
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it2.992.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 35

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.2-2.220.395320.313333365
2.22-2.240.37610.269464525
2.24-2.270.37410.264402443
2.27-2.290.244380.25428466
2.29-2.320.243510.213428479
2.32-2.340.321510.25456507
2.34-2.370.286500.205467517
2.37-2.40.277440.2442486
2.4-2.430.288450.194450495
2.43-2.460.215540.185465519
2.46-2.490.273400.202496536
2.49-2.530.297370.193455492
2.53-2.570.253510.189468519
2.57-2.610.29540.205449503
2.61-2.650.284460.218490536
2.65-2.70.296530.243450503
2.7-2.750.288610.205437498
2.75-2.80.239610.185474535
2.8-2.860.264420.201499541
2.86-2.920.269610.204442503
2.92-2.990.257590.201489548
2.99-3.060.24430.19455498
3.06-3.140.242490.209485534
3.14-3.240.242540.186490544
3.24-3.340.255550.207455510
3.34-3.460.256570.202482539
3.46-3.60.276490.2476525
3.6-3.760.268460.194501547
3.76-3.960.192490.177473522
3.96-4.210.193510.155497548
4.21-4.530.162600.148477537
4.53-4.990.151430.14501544
4.99-5.710.221590.196475534
5.71-7.20.213620.205483545
7.2-500.010.178580.173504562

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