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- PDB-7qrb: Crystal structure of CK1 delta in complex with PK-09-129 -

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Basic information

Entry
Database: PDB / ID: 7qrb
TitleCrystal structure of CK1 delta in complex with PK-09-129
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE / kinase / CK1d / inhibitor
Function / homology
Function and homology information


positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / tau-protein kinase / midbrain dopaminergic neuron differentiation / microtubule nucleation / protein localization to cilium / non-motile cilium assembly / protein localization to centrosome / COPII-mediated vesicle transport ...positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / tau-protein kinase / midbrain dopaminergic neuron differentiation / microtubule nucleation / protein localization to cilium / non-motile cilium assembly / protein localization to centrosome / COPII-mediated vesicle transport / tau-protein kinase activity / Golgi organization / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / endoplasmic reticulum-Golgi intermediate compartment membrane / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / spindle microtubule / circadian regulation of gene expression / regulation of circadian rhythm / spindle / Wnt signaling pathway / endocytosis / : / Regulation of PLK1 Activity at G2/M Transition / positive regulation of canonical Wnt signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / cilium / ciliary basal body / cadherin binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 ...: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-EX9 / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChaikuad, A. / Khirsariya, P. / Paruch, K. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Discovery of Potent and Exquisitely Selective Inhibitors of Kinase CK1 with Tunable Isoform Selectivity.
Authors: Nemec, V. / Khirsariya, P. / Janovska, P. / Moyano, P.M. / Maier, L. / Prochazkova, P. / Kebkova, P. / Gybel', T. / Berger, B.T. / Chaikuad, A. / Reinecke, M. / Kuster, B. / Knapp, S. / Bryja, V. / Paruch, K.
History
DepositionJan 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Casein kinase I isoform delta
B: Casein kinase I isoform delta
C: Casein kinase I isoform delta
D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,85519
Polymers137,6994
Non-polymers3,15515
Water4,504250
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1424
Polymers34,4251
Non-polymers7173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2385
Polymers34,4251
Non-polymers8134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2385
Polymers34,4251
Non-polymers8134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2385
Polymers34,4251
Non-polymers8134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.123, 84.588, 89.281
Angle α, β, γ (deg.)71.080, 74.100, 87.220
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 3 - 294 / Label seq-ID: 5 - 296

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Casein kinase I isoform delta / CKId / Tau-protein kinase CSNK1D


Mass: 34424.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EX9 / 3-(dimethylamino)-~{N}-[4-[4-(4-fluorophenyl)-5-(1~{H}-pyrrolo[2,3-b]pyridin-4-yl)imidazol-1-yl]cyclohexyl]propane-1-sulfonamide


Mass: 524.653 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33FN6O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 10% PEG 3350, 0.1M sodium sulfate, 0.1M citrate 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→49.53 Å / Num. obs: 37749 / % possible obs: 93.9 % / Redundancy: 3.4 % / CC1/2: 0.986 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.098 / Rrim(I) all: 0.185 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.6-2.740.4692.155890.7580.3670.6995.3
8.22-49.530.04812560.9970.030.05799.2

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RU8

6ru8


Resolution: 2.6→49.53 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.872 / SU B: 29.394 / SU ML: 0.315 / SU R Cruickshank DPI: 0.3382 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2734 1803 4.8 %RANDOM
Rwork0.2284 ---
obs0.2305 35942 93.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.08 Å2 / Biso mean: 35.131 Å2 / Biso min: 8.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20.06 Å2-0.44 Å2
2--0.67 Å2-0.73 Å2
3----0.41 Å2
Refinement stepCycle: final / Resolution: 2.6→49.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9502 0 203 250 9955
Biso mean--38.87 25.14 -
Num. residues----1162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139955
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179292
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.64213403
X-RAY DIFFRACTIONr_angle_other_deg1.1131.60221493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.53851163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67420.757555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.862151801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0811584
X-RAY DIFFRACTIONr_chiral_restr0.050.21196
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211442
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022314
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A93730.07
12B93730.07
21A96970.06
22C96970.06
31A98580.04
32D98580.04
41B95810.05
42C95810.05
51B93760.07
52D93760.07
61C96900.06
62D96900.06
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 154 -
Rwork0.3 2667 -
all-2821 -
obs--95.63 %
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)
12.2931-0.33210.50652.8914-1.53057.0299-0.1086-0.05720.0835-0.1042-0.04-0.1492-0.30680.16760.14860.10920.04220.00020.0445-0.00660.017818.607944.46531.0968
20.4865-0.3795-0.35510.63870.39071.29240.00630.0291-0.00260.0422-0.0028-0.0236-0.0429-0.0897-0.00350.05270.02810.01040.1086-0.02480.016429.459927.67515.6984
33.3296-0.1147-3.28429.82671.86133.71150.15090.4190.60990.00550.5288-0.9097-0.001-0.1585-0.67970.17040.12550.05780.3770.04850.281335.175938.747443.3384
40.7823-0.042-0.38820.15420.14761.26790.0677-0.01320.03990.04270.0229-0.0149-0.02540.0728-0.09060.04450.01050.01070.1042-0.0470.030520.585141.63762.2188
51.79640.00510.0120.00470.0731.560.0788-0.0109-0.08390.0010.0193-0.0073-0.06660.1932-0.09810.02290.00340.00270.1292-0.05920.03547.193478.71327.4168
60.8685-0.1552-0.02130.44560.38211.87020.08820.1095-0.0645-0.02820.0272-0.04660.11270.0263-0.11540.03850.0017-0.00940.0901-0.0510.0353-4.275770.095112.6791
70.58840.25540.30410.7730.63521.77490.047-0.05390.02840.06220.0167-0.05530.2177-0.2018-0.06370.0918-0.0429-0.01850.1414-0.00960.01251.130981.486158.4654
80.65720.3850.27710.3412-0.00661.6489-0.0044-0.0049-0.0665-0.03670.0194-0.07520.0580.0065-0.0150.059-0.01350.01120.0991-0.03660.028315.546390.661269.738
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 50
2X-RAY DIFFRACTION2A51 - 294
3X-RAY DIFFRACTION3B3 - 26
4X-RAY DIFFRACTION4B27 - 294
5X-RAY DIFFRACTION5C3 - 156
6X-RAY DIFFRACTION6C157 - 294
7X-RAY DIFFRACTION7D3 - 171
8X-RAY DIFFRACTION8D172 - 294

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