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- PDB-6fyk: X-Ray structure of CLK2-KD(136-496)/Indazole1 at 2.39A -

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Basic information

Entry
Database: PDB / ID: 6fyk
TitleX-Ray structure of CLK2-KD(136-496)/Indazole1 at 2.39A
ComponentsDual specificity protein kinase CLK2
KeywordsTRANSFERASE / SPLICING / PHOSPHOTRANSFERASE
Function / homology
Function and homology information


dual-specificity kinase / response to ionizing radiation / regulation of RNA splicing / negative regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / protein tyrosine kinase activity / protein autophosphorylation / nuclear body / nuclear speck / protein phosphorylation ...dual-specificity kinase / response to ionizing radiation / regulation of RNA splicing / negative regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / protein tyrosine kinase activity / protein autophosphorylation / nuclear body / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / identical protein binding / nucleus
Similarity search - Function
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 ...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 / Alpha Beta
Similarity search - Domain/homology
Chem-EAZ / Dual specificity protein kinase CLK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsKallen, J.
CitationJournal: ChemMedChem / Year: 2018
Title: X-ray Structures and Feasibility Assessment of CLK2 Inhibitors for Phelan-McDermid Syndrome.
Authors: Kallen, J. / Bergsdorf, C. / Arnaud, B. / Bernhard, M. / Brichet, M. / Cobos-Correa, A. / Elhajouji, A. / Freuler, F. / Galimberti, I. / Guibourdenche, C. / Haenni, S. / Holzinger, S. / ...Authors: Kallen, J. / Bergsdorf, C. / Arnaud, B. / Bernhard, M. / Brichet, M. / Cobos-Correa, A. / Elhajouji, A. / Freuler, F. / Galimberti, I. / Guibourdenche, C. / Haenni, S. / Holzinger, S. / Hunziker, J. / Izaac, A. / Kaufmann, M. / Leder, L. / Martus, H.J. / von Matt, P. / Polyakov, V. / Roethlisberger, P. / Roma, G. / Stiefl, N. / Uteng, M. / Lerchner, A.
History
DepositionMar 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 3, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all ..._reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all
Revision 1.4Jan 17, 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

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Assembly

Deposited unit
A: Dual specificity protein kinase CLK2
B: Dual specificity protein kinase CLK2
C: Dual specificity protein kinase CLK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,2766
Polymers128,3033
Non-polymers9733
Water8,395466
1
A: Dual specificity protein kinase CLK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0922
Polymers42,7681
Non-polymers3241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein kinase CLK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0922
Polymers42,7681
Non-polymers3241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity protein kinase CLK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0922
Polymers42,7681
Non-polymers3241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.633, 95.633, 222.858
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-701-

HOH

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Components

#1: Protein Dual specificity protein kinase CLK2 / CDC-like kinase 2


Mass: 42767.500 Da / Num. of mol.: 3 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P49760, dual-specificity kinase
#2: Chemical ChemComp-EAZ / (2~{S})-4-methyl-1-[5-(3-methyl-2~{H}-indazol-5-yl)pyridin-3-yl]oxy-pentan-2-amine


Mass: 324.420 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H24N4O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG2000, 0.2M trimethylamine n-oxide, 0.1M TRIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99986 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2016
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionResolution: 2.39→19.68 Å / Num. obs: 47518 / % possible obs: 99.8 % / Redundancy: 10 % / Biso Wilson estimate: 37.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.163 / Rrim(I) all: 0.171 / Net I/σ(I): 14.4
Reflection shellResolution: 2.39→2.45 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.927 / Mean I/σ(I) obs: 2.9 / CC1/2: 0.859 / Rrim(I) all: 0.981 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FYI

6fyi


Resolution: 2.39→19.68 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.441 / SU ML: 0.171 / SU R Cruickshank DPI: 0.5139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.514 / ESU R Free: 0.252
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 2376 5 %RANDOM
Rwork0.1948 ---
obs0.1964 45140 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 155.99 Å2 / Biso mean: 36.307 Å2 / Biso min: 14.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.04 Å20 Å2
2--0.04 Å20 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 2.39→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8709 0 72 466 9247
Biso mean--24.54 33.6 -
Num. residues----1047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0219076
X-RAY DIFFRACTIONr_angle_refined_deg0.9551.94812280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.12551072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88923.082490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.078151599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0551584
X-RAY DIFFRACTIONr_chiral_restr0.0690.21291
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217017
LS refinement shellResolution: 2.39→2.451 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 171 -
Rwork0.267 3263 -
all-3434 -
obs--100 %

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