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- PDB-9qsr: Protein Kinase CK2 and bivalent inhibitors -

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Basic information

Entry
Database: PDB / ID: 9qsr
TitleProtein Kinase CK2 and bivalent inhibitors
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Protein kinase inhibitor bivalent aD pocket
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 / histone H4S1 kinase activity / : / histone H3S57 kinase activity / histone H2BS14 kinase activity / histone H3S28 kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / ribosomal protein S6 kinase activity / histone H2AT120 kinase activity / histone H2BS36 kinase activity / eukaryotic translation initiation factor 2alpha 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 / Signal transduction by L1 / histone H3T45 kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / Hsp90 protein binding / PML body / Regulation of PTEN stability and activity / Wnt signaling pathway / KEAP1-NFE2L2 pathway / positive regulation of protein catabolic process / 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: 2.83 Å
AuthorsKrimm, I. / Gelin, M. / Guichou, J.F. / Grenier, D.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE18-0014-01 France
Agence Nationale de la Recherche (ANR)ANR-17-CONV-002 France
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Picomolar bivalent inhibitors of protein kinase CK2 active against beta-coronavirus replication.
Authors: Grenier, D. / Lopez Molina, D.S. / Gelin, M. / Mularoni, A. / Guichou, J.F. / Delcros, J.G. / Martinasso, C. / Yang, Y. / Ahnou, N. / Pawlotsky, J.M. / Ahmed-Belkacem, A. / Krimm, I.
History
DepositionApr 7, 2025Deposition 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
A: Casein kinase II subunit alpha
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,28210
Polymers85,5992
Non-polymers1,6838
Water27015
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6415
Polymers42,8001
Non-polymers8414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6415
Polymers42,8001
Non-polymers8414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.707, 128.707, 123.050
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-A1I90 / 5-[7-[(3-chloranyl-4-phenyl-phenyl)methylamino]heptylamino]benzo[c][2,6]naphthyridine-8-carboxylic acid


Mass: 553.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H33ClN4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.98 Å3/Da / Density % sol: 58.68 %
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: BM30A / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.83→128.71 Å / Num. obs: 45828 / % possible obs: 99.3 % / Redundancy: 11.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.045 / Rrim(I) all: 0.15 / Χ2: 0.99 / Net I/σ(I): 12.8
Reflection shellResolution: 2.83→2.98 Å / % possible obs: 97.4 % / Redundancy: 9.3 % / Rmerge(I) obs: 1.53 / Num. measured all: 32692 / Num. unique obs: 3526 / CC1/2: 0.727 / Rpim(I) all: 0.512 / Rrim(I) all: 1.618 / Χ2: 0.74 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→88.94 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 44.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3261 2294 5.01 %
Rwork0.268 --
obs0.2709 45828 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.83→88.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5467 0 110 15 5592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015725
X-RAY DIFFRACTIONf_angle_d1.1247759
X-RAY DIFFRACTIONf_dihedral_angle_d13.291773
X-RAY DIFFRACTIONf_chiral_restr0.059804
X-RAY DIFFRACTIONf_plane_restr0.013986
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-2.890.54081190.46892642X-RAY DIFFRACTION94
2.89-2.960.44721130.45082804X-RAY DIFFRACTION99
2.96-3.030.46741390.42662797X-RAY DIFFRACTION100
3.03-3.110.49371630.39272755X-RAY DIFFRACTION100
3.11-3.20.38361450.34882805X-RAY DIFFRACTION99
3.2-3.310.37591890.31462777X-RAY DIFFRACTION100
3.31-3.430.34691410.28882777X-RAY DIFFRACTION99
3.43-3.560.3851130.30312810X-RAY DIFFRACTION99
3.56-3.730.6419890.432116X-RAY DIFFRACTION74
3.73-3.920.39651640.30072658X-RAY DIFFRACTION96
3.92-4.170.26381810.22282725X-RAY DIFFRACTION99
4.17-4.490.25141210.20982804X-RAY DIFFRACTION100
4.49-4.940.25881450.18342818X-RAY DIFFRACTION100
4.94-5.660.26521480.21072784X-RAY DIFFRACTION100
5.66-7.120.27451590.23092786X-RAY DIFFRACTION100
7.13-88.940.26741650.20422676X-RAY DIFFRACTION96
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)
13.41530.99560.1691.90180.26622.654-0.02260.5494-0.53140.3873-0.0745-0.12540.67750.1240.06110.565-0.0343-0.02070.4126-0.07030.6371-3.3192-49.383916.3044
22.07092.78710.60984.28311.10920.3205-0.38781.58850.1763-1.2420.15310.0990.75680.15770.24740.6101-0.2280.11911.2614-0.00380.6905-4.5403-39.41360.2899
32.9533-0.4963-0.73971.84240.09622.2941-0.21440.5985-0.3281-0.09290.2785-0.26490.0953-0.1266-0.04360.6071-0.1878-0.04830.8252-0.07940.65115.9491-38.84915.2171
40.92661.17850.48893.58622.30892.03280.06080.14870.1127-1.08780.0390.0355-0.5665-0.2247-0.1490.7574-0.013-0.02250.75170.11570.505149.25152.8801-16.1619
51.28891.67410.28062.78030.48910.06991.4214-0.4412-0.81340.6295-1.92290.6134-0.19810.33320.55361.1142-0.10560.36511.1983-0.1820.849839.23864.3219-0.3423
61.51620.9719-0.72651.18720.70692.5930.0680.04960.0768-0.1297-0.04530.24240.1258-0.0963-0.01930.3480.09640.0030.49010.02490.567638.7199-16.3198-5.2624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 332 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 108 )
5X-RAY DIFFRACTION5chain 'B' and (resid 109 through 129 )
6X-RAY DIFFRACTION6chain 'B' and (resid 130 through 332 )

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