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- PDB-8vxd: Structure of Casein kinase I isoform delta (CK1d) complexed with ... -

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Basic information

Entry
Database: PDB / ID: 8vxd
TitleStructure of Casein kinase I isoform delta (CK1d) complexed with inhibitor 7
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / CK1D / KINASE / TRANSFERASE / 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 / 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 / COPII vesicle coating / midbrain dopaminergic neuron differentiation / 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 / spindle assembly / Major pathway of rRNA processing in the nucleolus and cytosol / 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 / 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
: / 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
Similarity search - Domain/homology
: / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsThompson, A.A. / Milligan, C.M. / Sharma, S.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Acs Med.Chem.Lett. / Year: 2024
Title: Structure-Based Optimization of Selective and Brain Penetrant CK1 delta Inhibitors for the Treatment of Circadian Disruptions.
Authors: McCarver, S. / Hanna, L. / Samant, A. / Thompson, A.A. / Seierstad, M. / Saha, A. / Wu, D. / Lord, B. / Sutton, S.W. / Shah, V. / Milligan, C.M. / Wennerholm, M. / Shelton, J. / Lebold, T.P. / Shireman, B.T.
History
DepositionFeb 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)70,1534
Polymers69,5662
Non-polymers5872
Water1629
1
A: Casein kinase I isoform delta
hetero molecules


  • defined by author
  • 35.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)35,0762
Polymers34,7831
Non-polymers2931
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


  • defined by author
  • 35.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)35,0762
Polymers34,7831
Non-polymers2931
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.556, 101.921, 66.891
Angle α, β, γ (deg.)90.00, 102.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34783.160 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 (E. coli)
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical ChemComp-A1AD7 / (4P)-4-[(3P)-3-(5-fluoropyridin-2-yl)-1-methyl-1H-pyrazol-4-yl]-1H-pyrrolo[2,3-b]pyridine


Mass: 293.298 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12FN5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 12%-20% PEG 10 K, 0.1 M Bis Tris (pH 5.5), 0.1 M Ammonium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.47→50.34 Å / Num. obs: 24239 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.04 / Rrim(I) all: 0.075 / Net I/σ(I): 8.8 / Num. measured all: 80884
Reflection shellResolution: 2.47→2.51 Å / % possible obs: 92.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.678 / Num. measured all: 3844 / Num. unique obs: 1116 / CC1/2: 0.603 / Rpim(I) all: 0.428 / Rrim(I) all: 0.804 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→50.34 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 40.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.295 1142 4.72 %
Rwork0.2649 --
obs0.2666 24182 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.47→50.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4449 0 44 9 4502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.314
X-RAY DIFFRACTIONf_dihedral_angle_d5.26641
X-RAY DIFFRACTIONf_chiral_restr0.078652
X-RAY DIFFRACTIONf_plane_restr0.011826
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.580.45241330.41182817X-RAY DIFFRACTION97
2.58-2.720.43351340.37172875X-RAY DIFFRACTION100
2.72-2.890.3861380.34542869X-RAY DIFFRACTION100
2.89-3.110.39731420.35122852X-RAY DIFFRACTION99
3.11-3.420.33971570.29372898X-RAY DIFFRACTION100
3.42-3.920.31971470.27142885X-RAY DIFFRACTION100
3.92-4.930.20951330.21142901X-RAY DIFFRACTION100
4.93-50.340.26481580.23452943X-RAY DIFFRACTION100
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)
14.1551-0.76110.62332.78740.78334.1761-0.2151-0.12250.29140.14630.16930.00890.15920.89460.08170.2720.0746-0.04060.5139-0.02420.3734-16.648542.819418.7011
25.3182-1.3219-0.30443.6527-1.15716.5504-0.3176-0.8228-0.32720.6250.2205-0.00831.26340.91270.01820.70750.3253-0.01440.8818-0.01720.4007-13.0234.427135.8837
32.4174-0.371-0.0310.3088-0.71913.4976-0.38-1.050.41650.64960.2806-0.2370.09842.32190.15840.79510.5026-0.31222.1521-0.24950.65321.143237.349834.0722
45.22510.27181.03165.02324.90917.7357-0.0982-0.46590.47180.29350.4064-0.44840.18350.9808-0.39060.4683-0.061-0.00270.96-0.13870.6947-5.633833.6863-0.0874
51.6940.494-0.28513.13721.95142.89120.00740.02130.1203-0.2057-0.29660.3607-0.1285-0.50180.27940.320.0026-0.110.435-0.00070.3364-25.347422.0831-5.2291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 147 )
2X-RAY DIFFRACTION2chain 'A' and (resid 148 through 222 )
3X-RAY DIFFRACTION3chain 'A' and (resid 223 through 293 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 59 )
5X-RAY DIFFRACTION5chain 'B' and (resid 60 through 298 )

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