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- PDB-8izc: Human CK1 Delta Kinase structure bound to Inhibitor -

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Basic information

Entry
Database: PDB / ID: 8izc
TitleHuman CK1 Delta Kinase structure bound to Inhibitor
ComponentsCasein kinase I isoform delta
KeywordsHYDROLASE/INHIBITOR / CK1 / kinase / inhibitor / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / midbrain dopaminergic neuron differentiation / COPII vesicle coating / microtubule nucleation / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / protein localization to centrosome / COPII-mediated vesicle transport ...positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / midbrain dopaminergic neuron differentiation / COPII vesicle coating / microtubule nucleation / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / 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 / cellular response to nerve growth factor stimulus / ciliary basal body / circadian regulation of gene expression / spindle microtubule / regulation of circadian rhythm / Wnt signaling pathway / spindle / endocytosis / Regulation of PLK1 Activity at G2/M Transition / Circadian Clock / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / positive regulation of protein phosphorylation / protein phosphorylation / 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
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: 1.45 Å
AuthorsGhosh, K.
Funding support India, 1items
OrganizationGrant numberCountry
Other private India
CitationJournal: To Be Published
Title: The Discovery of BMS-986164, a Potent, Selective and Orally Efficacious CK1d/e/a Inhibitor from Pyrazolo-Piperazine Chemotype
Authors: Velaparthi, U. / Selvakumar, K.
History
DepositionApr 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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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)68,8829
Polymers67,6142
Non-polymers1,2687
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-77 kcal/mol
Surface area25850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.999, 48.950, 82.052
Angle α, β, γ (deg.)95.75, 95.25, 106.12
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 33807.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Production host: Escherichia coli (E. coli)
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.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-S93 / ~{N}5-~{tert}-butyl-2-(3-chloranyl-4-fluoranyl-phenyl)-6,7-dihydro-4~{H}-pyrazolo[1,5-a]pyrazine-3,5-dicarboxamide


Mass: 393.843 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H21ClFN5O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.54 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M SODIUM SULPHATE, 0.100 M SODIUM CITRATE PH 5.5 , 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 113119 / % possible obs: 96.1 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 23
Reflection shellResolution: 1.45→14.62 Å / Rmerge(I) obs: 0.036 / Num. unique obs: 112996 / % possible all: 96.1

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALEPACKdata scaling
BUSTER2.11.5refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house structure

Resolution: 1.45→14.62 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.065 / SU Rfree Cruickshank DPI: 0.065
RfactorNum. reflection% reflectionSelection details
Rfree0.207 5665 5.01 %RANDOM
Rwork0.191 ---
obs0.192 112996 96.1 %-
Displacement parametersBiso mean: 25.81 Å2
Baniso -1Baniso -2Baniso -3
1--2.8443 Å2-3.4649 Å23.9716 Å2
2--0.2201 Å20.8752 Å2
3---2.6242 Å2
Refine analyzeLuzzati coordinate error obs: 0.176 Å
Refinement stepCycle: LAST / Resolution: 1.45→14.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4641 0 79 463 5183
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014889HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.986638HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1716SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes106HARMONIC2
X-RAY DIFFRACTIONt_gen_planes757HARMONIC5
X-RAY DIFFRACTIONt_it4889HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.72
X-RAY DIFFRACTIONt_other_torsion15.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion596SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6011SEMIHARMONIC4
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2506 432 5.28 %
Rwork0.227 7749 -
all0.2282 8181 -
obs--96.1 %

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