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- PDB-4g16: Crystal structure of ck1g3 with 2-[(4-{[3-(TRIFLUOROMETHYL)PYRIDI... -

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Basic information

Entry
Database: PDB / ID: 4g16
TitleCrystal structure of ck1g3 with 2-[(4-{[3-(TRIFLUOROMETHYL)PYRIDIN2-YL]OXY}PHENYL)AMINO]-1H-BENZIMIDAZOLE-6-CARBONITRILE
ComponentsCasein kinase I isoform gamma-3
KeywordsTRANSFERASE/TRANSFERASE inhibitor / ck1g / kinase / inhibitor / TRANSFERASE-TRANSFERASE inhibitor complex
Function / homology
Function and homology information


protein modification process / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding ...protein modification process / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Casein kinase 1 gamma C-terminal / Casein kinase 1 gamma C terminal / : / 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 ...Casein kinase 1 gamma C-terminal / Casein kinase 1 gamma C terminal / : / 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-0VM / Casein kinase I isoform gamma-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHuang, X.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: 2-Phenylamino-6-cyano-1H-benzimidazole-based isoform selective casein kinase 1 gamma (CK1g)inhibitors
Authors: Hua, Z. / Huang, X. / Bregman, H. / Chakka, N. / DiMauro, E.F. / Doherty, E.M. / Goldstein, J. / Gunaydin, H. / Huang, H. / Mercede, S. / Newcomb, J. / Patel, V.F. / Turci, S.M. / Yan, J. / ...Authors: Hua, Z. / Huang, X. / Bregman, H. / Chakka, N. / DiMauro, E.F. / Doherty, E.M. / Goldstein, J. / Gunaydin, H. / Huang, H. / Mercede, S. / Newcomb, J. / Patel, V.F. / Turci, S.M. / Yan, J. / Wilson, C. / Martin, M.W.
History
DepositionJul 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 gamma-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8652
Polymers38,4691
Non-polymers3951
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.153, 57.153, 223.431
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Casein kinase I isoform gamma-3 / CKI-gamma 3


Mass: 38469.223 Da / Num. of mol.: 1 / Fragment: unp residues 34-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1G3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y6M4, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-0VM / 2-[(4-{[3-(trifluoromethyl)pyridin-2-yl]oxy}phenyl)amino]-1H-benzimidazole-6-carbonitrile


Mass: 395.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H12F3N5O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 mM Tris, 0.2 M MgCl2, 2.5-15% PEG10K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 20688 / % possible obs: 92.1 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.089
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.403 / % possible all: 64.1

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IZR

2izr


Resolution: 2.3→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.25 967 RANDOM
Rwork0.237 --
obs-18826 -
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 29 221 2734

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