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- PDB-7qra: Crystal structure of CK1 delta in complex with VN725 -

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Basic information

Entry
Database: PDB / ID: 7qra
TitleCrystal structure of CK1 delta in complex with VN725
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 / midbrain dopaminergic neuron differentiation / tau-protein kinase / 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 / midbrain dopaminergic neuron differentiation / tau-protein kinase / 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 / 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 / endoplasmic reticulum-Golgi intermediate compartment membrane / AURKA Activation by TPX2 / ciliary basal body / spindle microtubule / circadian regulation of gene expression / cellular response to nerve growth factor stimulus / regulation of circadian rhythm / Wnt signaling pathway / spindle / endocytosis / Regulation of PLK1 Activity at G2/M Transition / positive regulation of canonical Wnt signaling pathway / Circadian Clock / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / Rho-dependent protein serine/threonine kinase activity / ribosomal protein S6 kinase activity / histone H2BS14 kinase activity / histone H3T6 kinase activity / histone H3T45 kinase activity / histone H3S10 kinase activity / histone H3T11 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of protein phosphorylation / cadherin binding / protein phosphorylation / protein serine/threonine kinase activity / protein serine kinase activity / centrosome / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...: / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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-EYI / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChaikuad, A. / Nemec, V. / 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

Downloads & links

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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)140,72228
Polymers137,6994
Non-polymers3,02324
Water5,999333
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2608
Polymers34,4251
Non-polymers8357
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3229
Polymers34,4251
Non-polymers8978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1016
Polymers34,4251
Non-polymers6775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0395
Polymers34,4251
Non-polymers6154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.208, 84.949, 90.070
Angle α, β, γ (deg.)70.840, 74.080, 86.930
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.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-EYI / 4-[3-cyclohexyl-5-(4-fluorophenyl)imidazol-4-yl]-1~{H}-pyrrolo[2,3-b]pyridine


Mass: 360.427 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H21FN4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 20% 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: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→49.74 Å / Num. obs: 48143 / % possible obs: 92.9 % / Redundancy: 2.9 % / CC1/2: 0.984 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.097 / Rrim(I) all: 0.172 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.532.80.3762.273460.8450.3070.53996.6
7.59-49.743.20.05115990.9970.0330.06297.4

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RU8

6ru8


Resolution: 2.4→49.74 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.859 / SU B: 23.3 / SU ML: 0.273 / SU R Cruickshank DPI: 0.7347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.735 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2816 2272 4.7 %RANDOM
Rwork0.2385 ---
obs0.2406 45677 92.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.99 Å2 / Biso mean: 32.3 Å2 / Biso min: 5.35 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20.64 Å20.07 Å2
2--2.17 Å2-1.66 Å2
3----1.45 Å2
Refinement stepCycle: final / Resolution: 2.4→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9270 0 198 333 9801
Biso mean--33.23 27.28 -
Num. residues----1138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0149664
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178714
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.66112980
X-RAY DIFFRACTIONr_angle_other_deg0.811.65620388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.27651128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49420.821536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.574151742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1991582
X-RAY DIFFRACTIONr_chiral_restr0.0580.21176
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211168
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021904
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A95640.05
12B95640.05
21A90280.07
22C90280.07
31A90360.07
32D90360.07
41B90370.07
42C90370.07
51B90320.07
52D90320.07
61C92450.05
62D92450.05
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 177 -
Rwork0.296 3550 -
all-3727 -
obs--96.03 %
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)
10.2746-0.2976-0.34720.44250.40861.06330.0360.03680.0213-0.01570.0087-0.0549-0.0429-0.1075-0.04480.05550.02210.01510.0828-0.04180.04415.7024-8.3968-14.7087
20.30580.30420.42490.32980.41061.19470.0555-0.0304-0.01790.01840.0101-0.03720.1001-0.1098-0.06550.0686-0.04340.00480.0869-0.04690.046410.176719.5184-50.8545
35.5830.7204-0.58421.0583-0.35341.6337-0.0152-0.07680.5125-0.07860.0390.06050.17650.4152-0.02380.02240.03650.00520.1677-0.04780.099238.4866-30.9579-65.3456
40.30450.0405-0.30220.40420.76791.94860.10920.04160.03250.01420.0809-0.0801-0.09450.0983-0.19020.05720.01130.01820.0913-0.07070.071318.7555-22.9738-50.1184
50.99950.41860.78760.25720.0042.00530.04760.1482-0.19630.03310.0707-0.1079-0.05850.2059-0.11840.0168-0.03230.01320.1498-0.11580.103734.520439.9144-6.3736
60.8019-0.0826-0.1250.18750.60882.30930.10760.0153-0.05180.00150.0333-0.06660.1196-0.0633-0.14090.0729-0.0388-0.00250.1017-0.06820.068920.256331.0435-18.5357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 294
2X-RAY DIFFRACTION2B3 - 294
3X-RAY DIFFRACTION3C3 - 81
4X-RAY DIFFRACTION4C82 - 294
5X-RAY DIFFRACTION5D3 - 176
6X-RAY DIFFRACTION6D177 - 294

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