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- PDB-9hl7: Protein Kinase CK2 and small molecule ligands -

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Basic information

Entry
Database: PDB / ID: 9hl7
TitleProtein Kinase CK2 and small molecule ligands
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Protein Kinase CK2 fragment ligand
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 / Maturation of hRSV A proteins ...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 / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / 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 / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H2AS121 kinase activity / histone H3S57 kinase activity / histone H3S28 kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / ribosomal protein S6 kinase activity / histone H2AT120 kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / histone H2BS36 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H3S10 kinase activity / AMP-activated protein kinase activity / histone H3T11 kinase activity / histone H3T3 kinase activity / 3-phosphoinositide-dependent protein kinase activity / histone H3T45 kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / 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 phosphorylation / 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: 2.28 Å
AuthorsKrimm, I. / Gelin, I. / Guichou, J.F.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CONV-002 France
Agence Nationale de la Recherche (ANR)ANR-21-CE18-0014-01 France
CitationJournal: Chemmedchem / Year: 2025
Title: Binding-Site Switch for Protein Kinase CK2 Inhibitors.
Authors: Grenier, D. / Gelin, M. / Yang, Y. / Mularoni, A. / Guichou, J.F. / Delcros, J.G. / Krimm, I.
History
DepositionDec 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Casein kinase II subunit alpha
C: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,09524
Polymers85,5992
Non-polymers2,49622
Water1,18966
1
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,96911
Polymers42,8001
Non-polymers1,17010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,12613
Polymers42,8001
Non-polymers1,32612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.949, 126.949, 124.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 42799.633 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-A1IVT / 2-(6-chloranyl-1~{H}-indol-3-yl)ethanoic acid


Mass: 209.629 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H8ClNO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 33 % polyethylene glycol methyl ether 5000, 0.2 M ammonium sulfate, 0.1 MES pH 6.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.28→56.77 Å / Num. obs: 141552 / % possible obs: 98.03 % / Redundancy: 3.1 % / CC1/2: 0.978 / Net I/σ(I): 8.5
Reflection shellResolution: 2.28→2.36 Å / Rmerge(I) obs: 1.064 / Num. unique obs: 4520 / CC1/2: 0.316

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→56.77 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2647 3583 4.31 %
Rwork0.2164 --
obs0.2185 83059 93.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→56.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5558 0 142 66 5766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095874
X-RAY DIFFRACTIONf_angle_d0.9997960
X-RAY DIFFRACTIONf_dihedral_angle_d7.053774
X-RAY DIFFRACTIONf_chiral_restr0.056810
X-RAY DIFFRACTIONf_plane_restr0.011012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.310.40731110.36872598X-RAY DIFFRACTION79
2.31-2.340.4331550.36482875X-RAY DIFFRACTION90
2.34-2.380.35441530.35623167X-RAY DIFFRACTION96
2.38-2.410.31661190.33873198X-RAY DIFFRACTION98
2.41-2.450.38361180.34593227X-RAY DIFFRACTION98
2.45-2.490.34871200.35493241X-RAY DIFFRACTION97
2.49-2.530.3431430.32223145X-RAY DIFFRACTION97
2.53-2.580.35711530.32023148X-RAY DIFFRACTION97
2.58-2.630.36951740.30013111X-RAY DIFFRACTION96
2.63-2.680.33641240.28913171X-RAY DIFFRACTION96
2.68-2.740.31711260.27353135X-RAY DIFFRACTION96
2.74-2.80.32141530.28063125X-RAY DIFFRACTION95
2.8-2.870.30471190.26683036X-RAY DIFFRACTION92
2.87-2.950.29471490.27572788X-RAY DIFFRACTION86
2.95-3.040.30361490.27313049X-RAY DIFFRACTION93
3.04-3.130.415810.25183179X-RAY DIFFRACTION96
3.14-3.250.31891630.23433040X-RAY DIFFRACTION93
3.25-3.380.26151770.21842934X-RAY DIFFRACTION91
3.38-3.530.26391310.21163198X-RAY DIFFRACTION97
3.53-3.720.25841430.20063150X-RAY DIFFRACTION97
3.72-3.950.226940.18263208X-RAY DIFFRACTION96
3.95-4.250.26751950.17113073X-RAY DIFFRACTION95
4.25-4.680.2231450.1663059X-RAY DIFFRACTION94
4.68-5.360.2121510.1732806X-RAY DIFFRACTION86
5.36-6.750.2304970.19782954X-RAY DIFFRACTION89
6.75-56.770.20661400.18752861X-RAY DIFFRACTION87
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.4124-1.65442.09031.419-0.21674.90940.22570.4832-0.135-0.3187-0.11050.03510.24990.4465-0.13510.4661-0.0414-0.00680.37830.00760.4735-1.5567-46.94948.574
25.6275-0.24864.57825.10232.24819.4213-0.14-1.1825-0.2670.2453-0.28070.0644-0.0149-0.13780.39440.51890.0324-0.01090.78470.12950.58069.8409-51.22323.1911
35.58760.14080.09976.23631.72144.7552-0.1927-0.6512-0.09470.44650.2037-0.2554-0.08150.4209-0.01030.37860.0896-0.04590.48740.0560.37054.752-45.744119.7339
43.1193-0.095-0.8322.32820.84342.8003-0.1947-0.3939-0.08290.44060.16170.09190.16550.08430.01960.55890.1195-0.01190.50980.03930.522-15.4299-38.899225.0785
51.13951.1848-0.24855.2239-2.23343.47640.0650.1546-0.1009-0.18190.02790.29560.2779-0.1633-0.090.58690.0235-0.03420.6023-0.08210.564314.842-65.8223-14.8186
63.39472.34890.20622.7806-0.26720.13770.731-1.4840.36411.0623-0.9456-0.1050.1582-0.1430.10070.7839-0.0848-0.15080.8373-0.01740.616124.5197-65.7274-0.0339
72.7969-0.00050.25823.249-0.15952.290.0529-0.1679-0.04720.2148-0.0254-0.1165-0.02440.1271-0.01890.3976-0.0417-0.01710.4240.00080.405525.5456-46.5437-4.6575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 44 )
2X-RAY DIFFRACTION2chain 'B' and (resid 45 through 74 )
3X-RAY DIFFRACTION3chain 'B' and (resid 75 through 129 )
4X-RAY DIFFRACTION4chain 'B' and (resid 130 through 332 )
5X-RAY DIFFRACTION5chain 'C' and (resid 2 through 108 )
6X-RAY DIFFRACTION6chain 'C' and (resid 109 through 129 )
7X-RAY DIFFRACTION7chain 'C' and (resid 130 through 332 )

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