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- PDB-8vxf: Structure of Casein kinase I isoform delta (CK1d) complexed with ... -

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Basic information

Entry
Database: PDB / ID: 8vxf
TitleStructure of Casein kinase I isoform delta (CK1d) complexed with inhibitor 15
Components(Casein kinase I isoform delta) x 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / CK1D / KINASE / TRANSFERASE / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / microtubule nucleation / midbrain dopaminergic neuron differentiation / 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 / microtubule nucleation / midbrain dopaminergic neuron differentiation / 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 / cytosol / cytoplasm
Similarity search - Function
: / 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 I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsThompson, A.A. / Milligan, C.M. / Sharma, S.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Acs Med.Chem.Lett. / Year: 2024
Title: Structure-Based Optimization of Selective and Brain Penetrant CK1 delta Inhibitors for the Treatment of Circadian Disruptions.
Authors: McCarver, S. / Hanna, L. / Samant, A. / Thompson, A.A. / Seierstad, M. / Saha, A. / Wu, D. / Lord, B. / Sutton, S.W. / Shah, V. / Milligan, C.M. / Wennerholm, M. / Shelton, J. / Lebold, T.P. / Shireman, B.T.
History
DepositionFeb 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3114
Polymers69,5822
Non-polymers7292
Water1448
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1642
Polymers34,7991
Non-polymers3641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1482
Polymers34,7831
Non-polymers3641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.127, 100.891, 65.958
Angle α, β, γ (deg.)90.00, 101.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34799.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Protein Casein kinase I isoform delta / CKI-delta / CKId / Tau-protein kinase CSNK1D


Mass: 34783.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#3: Chemical ChemComp-A1AD8 / (2P,3P,8S)-2-(5-fluoropyridin-2-yl)-6,6-dimethyl-3-(1H-pyrazolo[3,4-b]pyridin-4-yl)-6,7-dihydro-4H-pyrazolo[5,1-c][1,4]oxazine


Mass: 364.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H17FN6O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 12%-20% PEG 10 K, 0.1 M Bis Tris (pH 5.5), 0.1 M Ammonium Acetate

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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 EIGER X 9M / Detector: PIXEL / Date: Oct 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→54.38 Å / Num. obs: 29731 / % possible obs: 99.4 % / Redundancy: 3.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.062 / Rrim(I) all: 0.113 / Net I/σ(I): 5.8 / Num. measured all: 97642
Reflection shellResolution: 2.28→2.32 Å / % possible obs: 89.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 1.097 / Num. measured all: 4491 / Num. unique obs: 1331 / CC1/2: 0.523 / Rpim(I) all: 0.701 / Rrim(I) all: 1.305 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→44.18 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2707 1490 5.02 %
Rwork0.2255 --
obs0.2278 29691 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→44.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4584 0 54 8 4646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.515
X-RAY DIFFRACTIONf_dihedral_angle_d4.129650
X-RAY DIFFRACTIONf_chiral_restr0.038671
X-RAY DIFFRACTIONf_plane_restr0.003837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.350.39331170.37382419X-RAY DIFFRACTION94
2.35-2.440.34761340.33252587X-RAY DIFFRACTION100
2.44-2.540.35191350.31132536X-RAY DIFFRACTION99
2.54-2.650.33221430.27462558X-RAY DIFFRACTION100
2.65-2.790.29851470.25982545X-RAY DIFFRACTION100
2.79-2.970.33731240.26812591X-RAY DIFFRACTION100
2.97-3.190.32621340.24782575X-RAY DIFFRACTION100
3.19-3.520.26911410.22022574X-RAY DIFFRACTION100
3.52-4.020.23921430.20122593X-RAY DIFFRACTION100
4.02-5.070.22651400.16862592X-RAY DIFFRACTION100
5.07-44.180.22191320.20062631X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -2.6926 Å / Origin y: 23.4491 Å / Origin z: -43.2713 Å
111213212223313233
T0.3381 Å2-0.039 Å2-0.0433 Å2-0.2841 Å2-0.0389 Å2--0.4132 Å2
L0.1892 °2-0.168 °2-0.0851 °2-1.3257 °2-1.1937 °2--1.4065 °2
S-0.0569 Å °0.059 Å °-0.0284 Å °-0.0338 Å °0.0925 Å °-0.0608 Å °0.0897 Å °-0.202 Å °-0.0347 Å °
Refinement TLS groupSelection details: all

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