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

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Basic information

Entry
Database: PDB / ID: 2pvm
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 / 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 ...protein kinase CK2 complex / 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 / 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-P29 / 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. / 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)41,7962
Polymers41,4501
Non-polymers3451
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.638, 60.145, 44.984
Angle α, β, γ (deg.)90.000, 102.901, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-751-

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-P29 / 4-(2-(1H-IMIDAZOL-4-YL)ETHYLAMINO)-2-(PHENYLAMINO)PYRAZOLO[1,5-A][1,3,5]TRIAZINE-8-CARBONITRILE


Mass: 345.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15N9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12% PEG 4000, 0.10M Sodium Acetate, 0.10M TrisHCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 23, 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→50 Å / Num. all: 25306 / Num. obs: 25306 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.071 / Χ2: 1.052 / Net I/σ(I): 22.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 5.4 / Num. unique all: 2495 / Χ2: 1.039 / % possible all: 99.6

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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→50 Å / FOM work R set: 0.866 / Isotropic thermal model: ISOTROPIC / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2444 -RANDOM
Rwork0.184 ---
all0.188 24747 --
obs0.188 24747 100 %-
Displacement parametersBiso mean: 22.896 Å2
Baniso -1Baniso -2Baniso -3
1-5.513 Å20 Å22.11 Å2
2---7.622 Å20 Å2
3---2.109 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.261 Å0.212 Å
Luzzati d res low-5 Å
Luzzati sigma a0.192 Å0.144 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 26 265 3025
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0052
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.83
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it2.982.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 48

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2-2.010.29320.295309341
2.01-2.030.319470.25448495
2.03-2.040.26540.219469523
2.04-2.060.32450.239450495
2.06-2.070.216530.203456509
2.07-2.090.237510.195437488
2.09-2.110.278470.186456503
2.11-2.130.196350.191473508
2.13-2.140.301660.196457523
2.14-2.160.279480.199449497
2.16-2.180.199520.179426478
2.18-2.20.275460.194474520
2.2-2.220.238500.196474524
2.22-2.240.204390.181451490
2.24-2.270.213500.201483533
2.27-2.290.223490.178452501
2.29-2.310.282510.2460511
2.31-2.340.24490.172467516
2.34-2.370.251640.185445509
2.37-2.390.229550.188455510
2.39-2.420.235550.174470525
2.42-2.450.234520.169454506
2.45-2.490.235520.194478530
2.49-2.520.213540.179476530
2.52-2.560.199450.166458503
2.56-2.590.244590.195475534
2.59-2.630.331450.209466511
2.63-2.680.218470.194475522
2.68-2.720.246570.187462519
2.72-2.770.277560.193472528
2.77-2.830.205570.196451508
2.83-2.880.279540.189483537
2.88-2.950.248620.196451513
2.95-3.020.271430.197506549
3.02-3.090.221560.205433489
3.09-3.170.24580.219482540
3.17-3.270.235480.185495543
3.27-3.370.233600.194456516
3.37-3.490.212440.188491535
3.49-3.630.153530.171468521
3.63-3.80.183620.175477539
3.8-40.211510.166485536
4-4.250.153510.139479530
4.25-4.580.18430.138495538
4.58-5.040.182450.152495540
5.04-5.770.235510.197479530
5.77-7.270.256540.225491545
7.27-500.010.174470.161509556

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