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- PDB-8ae7: The strucuture of Compound 15 bound to CK2alpha -

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Basic information

Entry
Database: PDB / ID: 8ae7
TitleThe strucuture of Compound 15 bound to CK2alpha
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Fragment based drug discovery
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / : / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / rhythmic process / double-strand break repair / kinase activity / peptidyl-serine phosphorylation / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / regulation of cell cycle / protein stabilization / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / positive regulation of cell population proliferation / apoptotic process / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / 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
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / Chem-LVU / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.28 Å
AuthorsBrear, P. / De Fusco, C. / Atkinson, E. / Frances, N. / Iegre, J. / Venkitaraman, A. / Hyvonen, M. / Spring, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust090340/Z/09/Z United Kingdom
Wellcome Trust107714/Z/15/Z United Kingdom
CitationJournal: Rsc Med Chem / Year: 2022
Title: A fragment-based approach leading to the discovery of inhibitors of CK2 alpha with a novel mechanism of action.
Authors: Brear, P. / De Fusco, C. / Atkinson, E.L. / Iegre, J. / Francis-Newton, N.J. / Venkitaraman, A.R. / Hyvonen, M. / Spring, D.R.
History
DepositionJul 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)39,9496
Polymers39,0311
Non-polymers9185
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-19 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.553, 45.896, 63.471
Angle α, β, γ (deg.)90.000, 111.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 39031.391 Da / Num. of mol.: 1 / Mutation: K74A, K75A, K76A, R21S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P68400, non-specific serine/threonine protein kinase

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Non-polymers , 6 types, 344 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-LVU / 2-[5,6-bis(bromanyl)-1H-indazol-3-yl]ethanenitrile


Mass: 314.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H5Br2N3
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.28→59.02 Å / Num. obs: 80979 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 12.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.032 / Rrim(I) all: 0.081 / Net I/σ(I): 10.3 / Num. measured all: 517476 / Scaling rejects: 628
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.28-1.316.21.4223730259740.4920.6111.5511.1100
5.72-59.026.50.03762449620.9990.0160.04137.599.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
Aimless0.5.27data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PE1

3pe1


Resolution: 1.28→54.47 Å / Cor.coef. Fo:Fc: 0.9601 / Cor.coef. Fo:Fc free: 0.9493 / SU R Cruickshank DPI: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.058 / SU Rfree Blow DPI: 0.06 / SU Rfree Cruickshank DPI: 0.059
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 4039 5 %RANDOM
Rwork0.204 ---
obs0.2054 80700 99.76 %-
Displacement parametersBiso max: 107.38 Å2 / Biso mean: 20.2 Å2 / Biso min: 5.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.0054 Å20 Å20.2662 Å2
2---0.8156 Å20 Å2
3---0.8102 Å2
Refine analyzeLuzzati coordinate error obs: 0.196 Å
Refinement stepCycle: final / Resolution: 1.28→54.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 52 339 3139
Biso mean--30.16 28.86 -
Num. residues----327
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1047SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes462HARMONIC5
X-RAY DIFFRACTIONt_it2965HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion362SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3719SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2965HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4039HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion16.78
LS refinement shellResolution: 1.28→1.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 273 4.61 %
Rwork0.2758 5645 -
all0.276 5918 -
obs--99.76 %

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