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- PDB-4kb8: CK1d in complex with 1-{4-[3-(4-FLUOROPHENYL)-1-METHYL-1H-PYRAZOL... -

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Basic information

Entry
Database: PDB / ID: 4kb8
TitleCK1d in complex with 1-{4-[3-(4-FLUOROPHENYL)-1-METHYL-1H-PYRAZOL-4-YL]PYRIDIN-2-YL}-N-METHYLMETHANAMINE ligand
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 / 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 / spindle microtubule / circadian regulation of gene expression / regulation of circadian rhythm / spindle / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Circadian Clock / 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-1QN / N-benzyl-4-(pyridin-3-yl)pyrimidin-2-amine / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)156,03516
Polymers154,1494
Non-polymers1,88612
Water4,576254
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0264
Polymers38,5371
Non-polymers4883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9924
Polymers38,5371
Non-polymers4543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0264
Polymers38,5371
Non-polymers4883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9924
Polymers38,5371
Non-polymers4543
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)78,0178
Polymers77,0742
Non-polymers9436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3090 Å2
ΔGint-66 kcal/mol
Surface area24280 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)78,0178
Polymers77,0742
Non-polymers9436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area3240 Å2
ΔGint-67 kcal/mol
Surface area24940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.014, 84.541, 89.515
Angle α, β, γ (deg.)107.90, 105.87, 93.08
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-1QN / 1-{4-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]pyridin-2-yl}-N-methylmethanamine


Mass: 296.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H17FN4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-1QO / N-benzyl-4-(pyridin-3-yl)pyrimidin-2-amine


Mass: 262.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14N4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 43.51 %

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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: 1.95→81.12 Å / Num. all: 95216 / Num. obs: 91788 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 28.02 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 7.3

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Processing

SoftwareName: BUSTER / Version: 2.11.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.66 Å / Cor.coef. Fo:Fc: 0.9337 / Cor.coef. Fo:Fc free: 0.9126 / SU R Cruickshank DPI: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 4636 5.08 %RANDOM
Rwork0.2054 ---
obs0.2067 91271 96.39 %-
Displacement parametersBiso mean: 38.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.4508 Å20.07 Å2-0.3048 Å2
2---1.0917 Å2-3.5235 Å2
3---1.5425 Å2
Refine analyzeLuzzati coordinate error obs: 0.306 Å
Refinement stepCycle: LAST / Resolution: 1.95→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8999 0 124 254 9377
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019394HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0212665HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3320SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes203HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1473HARMONIC5
X-RAY DIFFRACTIONt_it9394HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion18.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1124SEMIHARMONIC5
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_contact10508SEMIHARMONIC4
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2436 322 4.84 %
Rwork0.2226 6336 -
all0.2236 6658 -
obs--96.39 %
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)
11.14590.2837-0.29180.5727-0.35841.92190.0403-0.11360.04940.01020.08910.1175-0.1433-0.2068-0.1294-0.16410.0270.03720.1410.1312-0.08370.0575-0.4651.1952
20.74920.1709-0.55790.3321-0.86042.29270.0778-0.05820.0630.0774-0.0663-0.0029-0.34960.318-0.0116-0.055-0.070.04340.06690.0537-0.106517.753416.8382-37.8833
31.3122-0.29390.18180.4463-0.49322.28650.04740.1-0.0671-0.00750.11450.12310.1282-0.3019-0.1619-0.1567-0.0187-0.00620.06930.1029-0.0856-0.3855-23.1127-41.5385
40.57-0.11370.44880.3597-0.80192.03940.07080.062-0.0304-0.0549-0.06850.00250.28490.3368-0.0023-0.06370.0767-0.00630.10450.071-0.118217.2059-39.4181-2.8006
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 D|401 - D|401 }B3 - 293
4X-RAY DIFFRACTION2{ B|3 - B|293 D|401 - D|401 }D401
5X-RAY DIFFRACTION3{ C|7 - C|293 C|401 - C|401 }C7 - 293
6X-RAY DIFFRACTION3{ C|7 - C|293 C|401 - C|401 }C401
7X-RAY DIFFRACTION4{ B|401 - B|401 D|3 - D|293 }B401
8X-RAY DIFFRACTION4{ B|401 - B|401 D|3 - D|293 }D3 - 293

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