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- PDB-4hni: crystal structure of ck1e in complex with PF4800567 -

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Basic information

Entry
Database: PDB / ID: 4hni
Titlecrystal structure of ck1e in complex with PF4800567
ComponentsCasein kinase I isoform epsilon
Keywordstransferase/transferase inhibitor / ck1e / kinase / inhibitor / PF4800567 / transferase-transferase inhibitor complex
Function / homology
Function and homology information


positive regulation of non-canonical Wnt signaling pathway / WNT mediated activation of DVL / circadian behavior / positive regulation of amyloid-beta formation / negative regulation of Wnt signaling pathway / Major pathway of rRNA processing in the nucleolus and cytosol / canonical Wnt signaling pathway / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes ...positive regulation of non-canonical Wnt signaling pathway / WNT mediated activation of DVL / circadian behavior / positive regulation of amyloid-beta formation / negative regulation of Wnt signaling pathway / Major pathway of rRNA processing in the nucleolus and cytosol / canonical Wnt signaling pathway / 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 / cellular response to nerve growth factor stimulus / negative regulation of protein binding / circadian regulation of gene expression / protein localization / regulation of circadian rhythm / endocytosis / regulation of protein localization / 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 / growth cone / non-specific serine/threonine protein kinase / protein kinase activity / ribonucleoprotein complex / protein phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / signal transduction / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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. ...Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-16W / Casein kinase I isoform epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsHuang, X. / Long, A.M. / Zhao, H.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Structural basis for the potent and selective inhibition of casein kinase 1 epsilon.
Authors: Long, A.M. / Zhao, H. / Huang, X.
History
DepositionOct 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Nov 7, 2018Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Casein kinase I isoform epsilon
B: Casein kinase I isoform epsilon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,21513
Polymers68,6312
Non-polymers1,58411
Water1,13563
1
A: Casein kinase I isoform epsilon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1567
Polymers34,3161
Non-polymers8406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Casein kinase I isoform epsilon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0606
Polymers34,3161
Non-polymers7445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.108, 111.108, 155.426
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 I isoform epsilon / CKI-epsilon / CKIe


Mass: 34315.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1E / Production host: Escherichia coli (E. coli)
References: UniProt: P49674, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-16W / 3-[(3-chlorophenoxy)methyl]-1-(tetrahydro-2H-pyran-4-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 359.810 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18ClN5O2 / Comment: inhibitor*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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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: 3.49 Å3/Da / Density % sol: 64.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Hepes, 3% Ethanol, 1.1-1.6 M (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-225 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.74→50 Å / Num. obs: 26206 / % possible obs: 100 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.146
Reflection shellResolution: 2.74→2.84 Å / Rmerge(I) obs: 0.685 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.273 1331 RANDOM
Rwork0.237 --
obs-26156 -
Refinement stepCycle: LAST / Resolution: 2.74→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4597 0 95 63 4755

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