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- PDB-4kbk: CK1d in complex with (3S)-3-{4-[3-(4-fluorophenyl)-1-methyl-1H-py... -

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Basic information

Entry
Database: PDB / ID: 4kbk
TitleCK1d in complex with (3S)-3-{4-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]pyridin-2-yl}morpholine inhibitor
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / ser/thr kinase / inhibitor / TRANSFERASE-TRANSFERASE 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
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-1QG / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiu, S.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Ligand-protein interactions of selective casein kinase 1 delta inhibitors.
Authors: Mente, S. / Arnold, E. / Butler, T. / Chakrapani, S. / Chandrasekaran, R. / Cherry, K. / Dirico, K. / Doran, A. / Fisher, K. / Galatsis, P. / Green, M. / Hayward, M. / Humphrey, J. / ...Authors: Mente, S. / Arnold, E. / Butler, T. / Chakrapani, S. / Chandrasekaran, R. / Cherry, K. / Dirico, K. / Doran, A. / Fisher, K. / Galatsis, P. / Green, M. / Hayward, M. / Humphrey, J. / Knafels, J. / Li, J. / Liu, S. / Marconi, M. / McDonald, S. / Ohren, J. / Paradis, V. / Sneed, B. / Walton, K. / Wager, T.
History
DepositionApr 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Feb 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

Downloads & links

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Assembly

Deposited unit
A: Casein kinase I isoform delta
B: Casein kinase I isoform delta
C: Casein kinase I isoform delta
D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,75121
Polymers154,1494
Non-polymers2,60217
Water10,863603
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2606
Polymers38,5371
Non-polymers7235
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1645
Polymers38,5371
Non-polymers6274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1645
Polymers38,5371
Non-polymers6274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1645
Polymers38,5371
Non-polymers6274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Casein kinase I isoform delta
hetero molecules

B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,42411
Polymers77,0742
Non-polymers1,3499
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area3830 Å2
ΔGint-101 kcal/mol
Surface area25750 Å2
MethodPISA
6
C: Casein kinase I isoform delta
hetero molecules

D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,32810
Polymers77,0742
Non-polymers1,2538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area3740 Å2
ΔGint-88 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.103, 84.760, 89.447
Angle α, β, γ (deg.)108.06, 105.85, 93.09
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: 38537.223 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical
ChemComp-1QG / (3S)-3-{4-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]pyridin-2-yl}morpholine


Mass: 338.379 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H19FN4O
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.66 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 72924 / Num. obs: 72584 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 2.38 % / Biso Wilson estimate: 31.97 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.14

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Processing

SoftwareName: BUSTER / Version: 2.11.5 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→17.21 Å / Cor.coef. Fo:Fc: 0.9387 / Cor.coef. Fo:Fc free: 0.9147 / SU R Cruickshank DPI: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3673 5.07 %RANDOM
Rwork0.1909 ---
obs0.1926 72486 95.38 %-
Displacement parametersBiso mean: 39.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.9352 Å20.312 Å2-0.3842 Å2
2---1.9261 Å2-6.4756 Å2
3---0.991 Å2
Refine analyzeLuzzati coordinate error obs: 0.271 Å
Refinement stepCycle: LAST / Resolution: 2.1→17.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9262 0 165 603 10030
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019717HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0113130HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3451SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes207HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1501HARMONIC5
X-RAY DIFFRACTIONt_it9717HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion18.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1161SEMIHARMONIC5
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_contact11066SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2441 253 5.14 %
Rwork0.2053 4667 -
all0.2072 4920 -
obs--95.38 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.90720.3844-0.32320.4762-0.5511.57090.00740.01410.1006-0.00210.01360.0182-0.28790.2377-0.0210.0199-0.07340.03520.00310.0116-0.042617.761416.8757-38.046
21.49440.21470.01330.5313-0.23761.8430.0576-0.20940.05810.02220.05660.1197-0.1151-0.2096-0.1142-0.08520.00720.02610.03370.052-0.0454-0.86010.1538-0.2099
31.5895-0.3311-0.0160.5187-0.22181.94450.07290.1873-0.0891-0.03420.06070.11040.1123-0.179-0.1335-0.0738-0.0238-0.03540.01310.0396-0.0345-0.1773-23.1603-41.0865
40.6624-0.20750.42270.3803-0.37131.38780.0103-0.0003-0.04920.02560.00630.00950.25760.2545-0.01660.01790.0773-0.02390.0480.0314-0.052517.3086-39.4077-2.7013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|293 A|401 - A|401 }A3 - 293
2X-RAY DIFFRACTION1{ A|3 - A|293 A|401 - A|401 }A401
3X-RAY DIFFRACTION2{ B|3 - B|293 B|401 - B|401 }B3 - 293
4X-RAY DIFFRACTION2{ B|3 - B|293 B|401 - B|401 }B401
5X-RAY DIFFRACTION3{ C|4 - C|293 C|401 - C|401 }C4 - 293
6X-RAY DIFFRACTION3{ C|4 - C|293 C|401 - C|401 }C401
7X-RAY DIFFRACTION4{ D|3 - D|293 D|401 - D|401 }D3 - 293
8X-RAY DIFFRACTION4{ D|3 - D|293 D|401 - D|401 }D401

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