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- PDB-9qy7: Crystal Structure of 54e bound to CK2a -

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Basic information

Entry
Database: PDB / ID: 9qy7
TitleCrystal Structure of 54e bound to CK2a
ComponentsCasein kinase II subunit alpha
KeywordsHYDROLASE / Fragment based drug discovery / kinase
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins ...regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of signal transduction by p53 class mediator / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Regulation of PTEN stability and activity / Wnt signaling pathway / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / kinase activity / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / 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 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsBrear, P. / Glossop, P. / Pandey, S. / Hyvonen, M. / Spring, D. / Butt, R. / Cawkill, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: J.Med.Chem. / Year: 2025
Title: Exploiting the Cryptic alpha D Pocket of Casein Kinase 2 alpha (CK2 alpha ) to Deliver Highly Potent and Selective Type 1 Inhibitors.
Authors: Glossop, P.A. / Brear, P. / Wright, S. / Flanagan, N. / Glossop, M.S. / Lane, C.A.L. / Butt, R.P. / Spring, D.R. / Hyvonen, M. / Cawkill, D.
History
DepositionApr 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)39,7114
Polymers39,0311
Non-polymers6803
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.295, 45.809, 63.064
Angle α, β, γ (deg.)90.00, 111.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-A1JB4 / 5-[2-[4-[[3-chloranyl-4-(trifluoromethyloxy)phenyl]methylamino]butoxy]ethylamino]benzo[c][2,6]naphthyridine-8-carboxamide


Mass: 561.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H27ClF3N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.01 Å3/Da / Density % sol: 38.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 112.5 mM MES pH 6.5, 35% glycerol ethoxylate and 180 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.39→49.96 Å / Num. obs: 62446 / % possible obs: 99.8 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.04 / Rrim(I) all: 0.085 / Χ2: 0.83 / Net I/σ(I): 9.6 / Num. measured all: 275869
Reflection shellResolution: 1.39→1.46 Å / % possible obs: 99.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 2.022 / Num. measured all: 39546 / Num. unique obs: 9036 / CC1/2: 0.371 / Rpim(I) all: 1.075 / Rrim(I) all: 2.298 / Χ2: 0.71 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→49.96 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.067 / SU Rfree Cruickshank DPI: 0.066
RfactorNum. reflection% reflectionSelection details
Rfree0.208 3098 5.01 %RANDOM
Rwork0.182 ---
obs0.183 61802 98.9 %-
Displacement parametersBiso mean: 26.07 Å2
Baniso -1Baniso -2Baniso -3
1-1.2789 Å20 Å24.4305 Å2
2---2.0985 Å20 Å2
3---0.8196 Å2
Refinement stepCycle: 1 / Resolution: 1.39→49.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 47 322 3117
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012948HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.994005HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1043SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes461HARMONIC5
X-RAY DIFFRACTIONt_it2948HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.39
X-RAY DIFFRACTIONt_other_torsion16.55
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion352SEMIHARMONIC5
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_contact3818SEMIHARMONIC4
LS refinement shellResolution: 1.39→1.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2801 196 4.82 %
Rwork0.2639 3868 -
all0.2646 4064 -
obs--88.89 %

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