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- PDB-11uc: Crystal structure of Casein Kinase 2 (CK2) alpha in complex with ... -

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Basic information

Entry
Database: PDB / ID: 11uc
TitleCrystal structure of Casein Kinase 2 (CK2) alpha in complex with BMS-595
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / KINASE / CSNK2A1 / CKII / CK2A1 / CKII ALPHA
Function / homology
Function and homology information


Phosphorylation and nuclear translocation of BMAL1 (ARNTL) and CLOCK / positive regulation of aggrephagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Phosphorylation and nuclear translocation of the CRY:PER:kinase complex / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / Receptor Mediated Mitophagy ...Phosphorylation and nuclear translocation of BMAL1 (ARNTL) and CLOCK / positive regulation of aggrephagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Phosphorylation and nuclear translocation of the CRY:PER:kinase complex / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / negative regulation of signal transduction by p53 class mediator / 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 / negative regulation of double-strand break repair via homologous recombination / positive regulation of Wnt signaling pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / kinase activity / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / rhythmic process / double-strand break repair / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / protein folding / 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 / apoptotic process / positive regulation of cell population proliferation / 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
: / : / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.962 Å
AuthorsTararina, M.A. / Witmer, M.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2026
Title: Discovery of BMS-159, an Orally Active Imidazotriazine Pan-CK2 Inhibitor for the Treatment of Cancer.
Authors: Tarby, C.M. / Hart, A. / Wan, H. / He, L. / Tokarski, J. / Fink, B. / Zhao, Y. / Huynh, T. / Gavai, A. / Zimmermann, K. / Vite, G. / Vyas, D. / Inghrim, J. / Obermeier, M. / Fura, A. / ...Authors: Tarby, C.M. / Hart, A. / Wan, H. / He, L. / Tokarski, J. / Fink, B. / Zhao, Y. / Huynh, T. / Gavai, A. / Zimmermann, K. / Vite, G. / Vyas, D. / Inghrim, J. / Obermeier, M. / Fura, A. / Elzinga, P. / Hunt, J. / Roongta, U. / Henley, B. / Lippy, J. / Mathur, A. / Wu, D.R. / Li, P. / Raghavan, N. / Everlof, G. / Rupnow, B. / Lee, F. / Fargnoli, J. / Tredup, J. / Kiefer, S.E. / Calambur, D. / Gupta, A. / Vetrichelvan, M. / Subbaiah, M.A.M. / Purandare, A.V.
History
DepositionMar 13, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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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)40,6534
Polymers40,0671
Non-polymers5863
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.284, 78.875, 82.073
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 40066.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1DAS / methyl [4-chloro-3-{[(4S)-3-cyano-8-(cyclopropylamino)imidazo[1,2-b]pyridazin-6-yl]amino}-5-(4-methylpiperazin-1-yl)phenyl]carbamate


Mass: 495.965 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26ClN9O2
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 1.95 Å3/Da / Density % sol: 36.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Tris-HCl pH 7.0, 0.2 M MnCl2, 16% PEG 5,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→41.62 Å / Num. obs: 22831 / % possible obs: 99.1 % / Redundancy: 6.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.055 / Rrim(I) all: 0.14 / Net I/σ(I): 11.9
Reflection shellResolution: 1.96→2.05 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.484 / Num. unique obs: 3260 / Rpim(I) all: 0.223 / Rrim(I) all: 0.571

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Processing

Software
NameVersionClassification
PHENIXdev_780refinement
SCALAdata scaling
XDSdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.962→41.036 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 19.41 / Stereochemistry target values: ML
Details: The free-R subset flag in the structure factor file is incorrect.
RfactorNum. reflection% reflection
Rfree0.2147 1855 4.35 %
Rwork0.1604 --
obs0.1627 22826 98.52 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.016 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9638 Å20 Å2-0 Å2
2--2.8045 Å2-0 Å2
3----1.8407 Å2
Refinement stepCycle: LAST / Resolution: 1.962→41.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2675 0 37 259 2971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072821
X-RAY DIFFRACTIONf_angle_d1.013849
X-RAY DIFFRACTIONf_dihedral_angle_d15.711042
X-RAY DIFFRACTIONf_chiral_restr0.075409
X-RAY DIFFRACTIONf_plane_restr0.004491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.962-2.01480.2431430.18693071X-RAY DIFFRACTION97
2.0148-2.07410.28541400.17363145X-RAY DIFFRACTION99
2.0741-2.14110.23081410.17173112X-RAY DIFFRACTION98
2.1411-2.21760.25681400.17543103X-RAY DIFFRACTION98
2.2176-2.30640.26021400.17743146X-RAY DIFFRACTION98
2.3064-2.41130.22461440.17093155X-RAY DIFFRACTION99
2.4113-2.53840.23841410.16353129X-RAY DIFFRACTION99
2.5384-2.69750.24591450.17493180X-RAY DIFFRACTION99
2.6975-2.90570.22351400.16663143X-RAY DIFFRACTION99
2.9057-3.1980.21851460.1583160X-RAY DIFFRACTION99
3.198-3.66050.19921380.1463155X-RAY DIFFRACTION99
3.6605-4.61080.15021470.12753161X-RAY DIFFRACTION99
4.6108-41.0360.18911500.16193165X-RAY DIFFRACTION99

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