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- PDB-4twc: 2-Benzamido-N-(1H-benzo[d]imidazol-2-yl)thiazole-4- carboxamide d... -

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Basic information

Entry
Database: PDB / ID: 4twc
Title2-Benzamido-N-(1H-benzo[d]imidazol-2-yl)thiazole-4- carboxamide derivatives as potent inhibitors of CK1d/e
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE / CK1d / CK1e / Phosphorylation / Small molecule 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 / microtubule nucleation / protein localization to cilium / tau-protein kinase / 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 / microtubule nucleation / protein localization to cilium / tau-protein kinase / 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 / 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 / positive regulation of canonical Wnt signaling pathway / Circadian Clock / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / 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
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-37J / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBischof, J. / Leban, L. / Zaja, M. / Grothey, A. / Radunsky, B. / Othersen, O. / Strobl, S. / Vitt, D. / Knippschild, U.
CitationJournal: Amino Acids / Year: 2012
Title: 2-Benzamido-N-(1H-benzo[d]imidazol-2-yl)thiazole-4-carboxamide derivatives as potent inhibitors of CK1d/e.
Authors: Bischof, J. / Leban, J. / Zaja, M. / Grothey, A. / Radunsky, B. / Othersen, O. / Strobl, S. / Vitt, D. / Knippschild, U.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,36018
Polymers68,6212
Non-polymers2,73816
Water15,079837
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8879
Polymers34,3111
Non-polymers1,5768
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4739
Polymers34,3111
Non-polymers1,1628
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.040, 134.721, 56.845
Angle α, β, γ (deg.)90.000, 99.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

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


Mass: 34310.613 Da / Num. of mol.: 2 / Mutation: R13N
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
#4: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 851 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-37J / 2-{[2-(trifluoromethoxy)benzoyl]amino}-N-[6-(trifluoromethyl)-1H-benzimidazol-2-yl]-1,3-thiazole-4-carboxamide


Mass: 515.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H11F6N5O3S
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 837 / 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: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1 M NaCl, 1.4 M (NH4)2SO4, 0.1 M Bis-Tris, pH 5.8

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→28.87 Å / Num. obs: 82702 / % possible obs: 97.9 % / Redundancy: 2.3 % / Net I/σ(I): 10.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
ADSCdata collection
SCALAdata scaling
PDB_EXTRACT3.14data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CKI

1cki


Resolution: 1.7→19.73 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.793 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 4085 4.9 %RANDOM
Rwork0.1628 78490 --
obs0.1648 78490 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 112.77 Å2 / Biso mean: 29.498 Å2 / Biso min: 12.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å20.02 Å2
2--0.39 Å20 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 1.7→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4790 0 172 837 5799
Biso mean--41.4 41.89 -
Num. residues----585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195198
X-RAY DIFFRACTIONr_bond_other_d0.0010.024943
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.9977025
X-RAY DIFFRACTIONr_angle_other_deg0.957311383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6655624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15222.863248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27615938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2721543
X-RAY DIFFRACTIONr_chiral_restr0.1470.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025762
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021291
X-RAY DIFFRACTIONr_mcbond_it3.0142.4362380
X-RAY DIFFRACTIONr_mcbond_other3.0132.4352379
X-RAY DIFFRACTIONr_mcangle_it4.2473.6292979
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 308 -
Rwork0.34 5819 -
all-6127 -
obs--98.58 %

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