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- PDB-6hmr: Crystal structure of human Casein Kinase I delta in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6hmr
TitleCrystal structure of human Casein Kinase I delta in complex with a photoswitchable 2-Azothiazole-based inhibitor (compound 2)
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE / Kinase / Photoswitchable 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 / tau-protein kinase / microtubule nucleation / protein localization to cilium / 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 / tau-protein kinase / microtubule nucleation / protein localization to cilium / 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 / ciliary basal body / spindle microtubule / circadian regulation of gene expression / cellular response to nerve growth factor stimulus / 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 / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / Rho-dependent protein serine/threonine kinase activity / ribosomal protein S6 kinase activity / histone H2BS14 kinase activity / histone H3T6 kinase activity / histone H3T45 kinase activity / histone H3S10 kinase activity / histone H3T11 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of protein phosphorylation / cadherin binding / protein phosphorylation / protein serine/threonine kinase activity / protein serine kinase activity / centrosome / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...: / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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-GE5 / MALONIC ACID / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.782 Å
AuthorsPichlo, C. / Schehr, M. / Charl, J. / Brunstein, E. / Peifer, C. / Baumann, U.
CitationJournal: Photochem. Photobiol. Sci. / Year: 2019
Title: 2-Azo-, 2-diazocine-thiazols and 2-azo-imidazoles as photoswitchable kinase inhibitors: limitations and pitfalls of the photoswitchable inhibitor approach.
Authors: Schehr, M. / Ianes, C. / Weisner, J. / Heintze, L. / Muller, M.P. / Pichlo, C. / Charl, J. / Brunstein, E. / Ewert, J. / Lehr, M. / Baumann, U. / Rauh, D. / Knippschild, U. / Peifer, C. / Herges, R.
History
DepositionSep 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)74,0996
Polymers72,7562
Non-polymers1,3434
Water8,323462
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0503
Polymers36,3781
Non-polymers6722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0503
Polymers36,3781
Non-polymers6722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.880, 74.036, 89.485
Angle α, β, γ (deg.)90.00, 102.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36377.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical ChemComp-GE5 / 3-(2,5-dimethoxyphenyl)-~{N}-[4-[4-(4-fluorophenyl)-2-[(~{E})-phenyldiazenyl]-1,3-thiazol-5-yl]pyridin-2-yl]propanamide


Mass: 567.633 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H26FN5O3S
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium malonate pH 6.0 20 % Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000031 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 1.782→46.38 Å / Num. obs: 57955 / % possible obs: 97.37 % / Redundancy: 7 % / Net I/σ(I): 11.23
Reflection shellResolution: 1.782→1.846 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: 000)refinement
XDS20180126data reduction
XDS20180126data scaling
PHASER(1.12_2829: 000)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MQV

5mqv


Resolution: 1.782→46.38 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 23.23
RfactorNum. reflection% reflection
Rfree0.1993 1896 3.27 %
Rwork0.1751 --
obs0.1759 57936 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.782→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4589 0 96 462 5147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074848
X-RAY DIFFRACTIONf_angle_d0.8496532
X-RAY DIFFRACTIONf_dihedral_angle_d13.472846
X-RAY DIFFRACTIONf_chiral_restr0.05671
X-RAY DIFFRACTIONf_plane_restr0.006836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7817-1.82620.33131190.33993849X-RAY DIFFRACTION94
1.8262-1.87560.341480.3013960X-RAY DIFFRACTION96
1.8756-1.93080.30211290.28833904X-RAY DIFFRACTION96
1.9308-1.99310.27591370.24573933X-RAY DIFFRACTION96
1.9931-2.06430.26271370.223991X-RAY DIFFRACTION97
2.0643-2.1470.21351340.19843970X-RAY DIFFRACTION97
2.147-2.24470.23071250.18374013X-RAY DIFFRACTION97
2.2447-2.36310.23891510.18143991X-RAY DIFFRACTION97
2.3631-2.51110.17741280.16823996X-RAY DIFFRACTION98
2.5111-2.7050.19161380.16094045X-RAY DIFFRACTION98
2.705-2.97710.19481380.16164043X-RAY DIFFRACTION98
2.9771-3.40780.17511410.15364075X-RAY DIFFRACTION99
3.4078-4.29310.15371340.13794087X-RAY DIFFRACTION99
4.2931-47.67930.16521370.1534183X-RAY DIFFRACTION99
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)
17.45091.86324.19882.42770.6924.5889-0.12910.09410.2754-0.10310.0887-0.0313-0.33690.07840.02160.1879-0.01610.06170.25910.01350.219311.41995.616716.365
23.37134.5352.6067.63451.58124.8849-0.06840.0561-0.2209-0.03590.0404-0.40290.2870.30550.04240.1810.02180.04530.2135-0.00740.21988.7671-6.901424.6405
33.40154.4252-2.35126.8925-1.22297.08220.02370.5337-0.55950.0347-0.0686-0.61740.34310.34090.08460.15520.03840.04490.3535-0.01090.342914.84440.005616.3884
40.85030.90480.98465.90710.66725.65880.2404-0.10450.4508-0.13250.00410.038-0.37030.0577-0.16660.126-0.007-0.00340.15340.02690.1099-10.52098.129521.0127
52.8378-0.83631.15121.1641-0.73113.520.03710.0873-0.1264-0.0793-0.0051-0.0730.23110.2702-0.0460.1405-0.0120.01180.127-0.01060.1672-1.1959-4.5431.1386
61.3295-0.50711.35072.3403-1.71584.6644-0.0121-0.0770.0520.1169-0.0264-0.1828-0.29350.20780.06890.1617-0.02220.01420.2026-0.01290.1578-2.22655.195240.6294
78.05431.32920.42566.4382-2.35357.35430.2048-0.4360.58860.3876-0.1872-0.2662-0.71740.48710.02930.3217-0.01530.04290.2555-0.06490.308-4.443717.772242.1089
82.824-0.73070.32831.821-0.41093.48080.0403-0.3136-0.03460.06930.01470.0832-0.0965-0.3077-0.06960.1446-0.02220.01180.29020.01030.1484-12.73720.462443.5956
92.5879-0.50411.68280.35180.30632.59350.1118-0.0988-0.3741-0.0177-0.03230.11050.3001-0.3322-0.12910.1722-0.0486-0.00020.1982-0.00130.2305-18.9302-4.805627.5898
102.8610.38070.22313.38812.33177.2521-0.0466-0.45340.17120.42210.02360.3058-0.3877-0.40210.04290.38150.03230.06450.37040.0010.25345.9937-26.5429-4.4426
114.41861.51710.5154.3048-2.7877.0221-0.1995-0.03740.12290.3501-0.136-0.2157-0.62140.72450.2480.2653-0.03460.00270.41120.01160.262310.7712-31.19967.7887
123.98473.8136-3.2224.7022-5.388.9418-0.02810.44450.27240.5011-0.3094-0.2988-0.76991.10170.25040.4685-0.0627-0.03490.75520.08260.419412.9798-26.93751.5762
131.95090.6081.06230.99480.25142.9638-0.05580.0624-0.0441-0.02470.0582-0.0795-0.00830.2956-0.02590.16460.03460.01470.22860.00770.1623-0.4114-37.964815.4819
141.94321.08540.57042.71181.06294.08170.0155-0.06980.2622-0.0273-0.01130.0349-0.30240.0911-0.00120.19050.03090.02270.20560.00190.1677-4.648-29.622725.3665
154.28022.8819-0.00544.9523-0.13654.80960.175-0.00530.30950.2038-0.16580.18-0.4177-0.46230.02150.20560.10970.03050.33790.00860.2322-17.5445-30.678226.4349
164.29573.36042.42224.98911.93744.4410.1245-0.2920.01320.2244-0.0477-0.04810.18210.2147-0.05630.18770.01610.01250.2620.01060.1435-4.6853-39.530831.7912
179.23939.25488.76049.51358.73848.26870.10120.1117-0.35910.13040.1062-0.16930.37380.1123-0.13830.24180.02160.00460.19110.06450.2103-8.1001-50.791423.7431
184.8874.6633-3.99028.0429-4.45553.3817-0.11650.4716-0.3652-0.33920.27510.10040.2672-0.6488-0.21140.2629-0.0033-0.0360.2951-0.03570.2502-13.2981-49.74278.4636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 101 )
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 167 )
6X-RAY DIFFRACTION6chain 'A' and (resid 168 through 208 )
7X-RAY DIFFRACTION7chain 'A' and (resid 209 through 234 )
8X-RAY DIFFRACTION8chain 'A' and (resid 235 through 265 )
9X-RAY DIFFRACTION9chain 'A' and (resid 266 through 294 )
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 32 )
11X-RAY DIFFRACTION11chain 'B' and (resid 33 through 67 )
12X-RAY DIFFRACTION12chain 'B' and (resid 68 through 83 )
13X-RAY DIFFRACTION13chain 'B' and (resid 84 through 167 )
14X-RAY DIFFRACTION14chain 'B' and (resid 168 through 208 )
15X-RAY DIFFRACTION15chain 'B' and (resid 209 through 246 )
16X-RAY DIFFRACTION16chain 'B' and (resid 247 through 265 )
17X-RAY DIFFRACTION17chain 'B' and (resid 266 through 279 )
18X-RAY DIFFRACTION18chain 'B' and (resid 280 through 293 )

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