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- PDB-6ytw: CLK3 bound with benzothiazole Tg003 (Cpd 2) -

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Basic information

Entry
Database: PDB / ID: 6ytw
TitleCLK3 bound with benzothiazole Tg003 (Cpd 2)
ComponentsDual specificity protein kinase CLK3
KeywordsTRANSFERASE / Inhibitor / Complex / CLK3 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / nuclear speck / protein phosphorylation / protein serine kinase activity ...dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane
Similarity search - Function
: / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; 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. ...: / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; 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 / Alpha Beta
Similarity search - Domain/homology
Chem-EAE / PHOSPHATE ION / Dual specificity protein kinase CLK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchroeder, M. / Chaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2020
Title: DFG-1 Residue Controls Inhibitor Binding Mode and Affinity, Providing a Basis for Rational Design of Kinase Inhibitor Selectivity.
Authors: Schroder, M. / Bullock, A.N. / Fedorov, O. / Bracher, F. / Chaikuad, A. / Knapp, S.
History
DepositionApr 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein kinase CLK3
B: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,57026
Polymers84,6372
Non-polymers1,93324
Water9,620534
1
A: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,25713
Polymers42,3181
Non-polymers93812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,31313
Polymers42,3181
Non-polymers99512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.057, 131.599, 83.598
Angle α, β, γ (deg.)90.000, 107.980, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-511-

PO4

21B-501-

PO4

31A-913-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dual specificity protein kinase CLK3 / CDC-like kinase 3


Mass: 42318.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK3 / Production host: Escherichia coli (E. coli) / References: UniProt: P49761, dual-specificity kinase

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Non-polymers , 6 types, 558 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-EAE / (1~{Z})-1-(3-ethyl-5-methoxy-1,3-benzothiazol-2-ylidene)propan-2-one


Mass: 249.329 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H15NO2S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 21% PEG 3350, 0,2M Na/K PO4, 10% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→50.69 Å / Num. obs: 66435 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.045 / Rrim(I) all: 0.114 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.056.70.6532989844750.8390.2710.7082.8100
9.38-50.696.10.04840966750.9970.0210.05330.399.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2eu9

2eu9


Resolution: 2→50.69 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.571 / SU ML: 0.124 / SU R Cruickshank DPI: 0.1533 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.146
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 3266 4.9 %RANDOM
Rwork0.1839 ---
obs0.186 63166 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.29 Å2 / Biso mean: 33.782 Å2 / Biso min: 17.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20.2 Å2
2---0.08 Å20 Å2
3----0.32 Å2
Refinement stepCycle: final / Resolution: 2→50.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5589 0 123 534 6246
Biso mean--47.89 39.22 -
Num. residues----688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135944
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175428
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.6488007
X-RAY DIFFRACTIONr_angle_other_deg1.3831.58212545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1095704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11821.55342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.977151012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3791544
X-RAY DIFFRACTIONr_chiral_restr0.090.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026770
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021342
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 251 -
Rwork0.254 4646 -
all-4897 -
obs--99.98 %
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)
10.16540.0382-0.05940.8327-0.92393.7677-0.03350.1454-0.0166-0.10830.0288-0.04920.22370.28750.00470.33670.0363-0.01020.178-0.02860.066813.35297.98263.9015
21.43620.15530.2351.2481-0.23050.735-0.19430.07220.80150.0765-0.0542-0.1548-0.22570.18460.24850.3809-0.05-0.17150.04670.06850.503815.3521139.107323.4792
31.83141.36081.21081.02760.90433.0184-0.17930.15460.3939-0.19710.10310.3236-0.4373-0.51250.07630.52560.1163-0.09510.19060.06380.1662-6.821142.786512.0314
40.970.8320.0843.51940.03021.14240.2205-0.15-0.48820.1194-0.1121-0.08340.42740.0469-0.10840.42630.0182-0.2080.03070.06510.30863.7498100.010428.5937
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A126 - 294
2X-RAY DIFFRACTION2A295 - 480
3X-RAY DIFFRACTION3B134 - 298
4X-RAY DIFFRACTION4B309 - 481

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