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- PDB-6yte: CLK1 bound with benzothiazole Tg003 (Cpd 2) -

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Basic information

Entry
Database: PDB / ID: 6yte
TitleCLK1 bound with benzothiazole Tg003 (Cpd 2)
ComponentsDual specificity protein kinase CLK1
KeywordsTRANSFERASE / Inhibitor / Complex / CLK1 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


dual-specificity kinase / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / non-membrane spanning protein tyrosine kinase activity / protein tyrosine kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP 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. ...: / 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-EAE / Dual specificity protein kinase CLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 / 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
C: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8312
Polymers39,5821
Non-polymers2491
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.719, 64.269, 73.103
Angle α, β, γ (deg.)90.000, 117.730, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Dual specificity protein kinase CLK1 / CDC-like kinase 1


Mass: 39581.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK1, CLK / Production host: Escherichia coli (E. coli) / References: UniProt: P49759, dual-specificity kinase
#2: 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.: 1 / Source method: obtained synthetically / Formula: C13H15NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 26% PEG 6k, 0.1M bicine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.3→46.9 Å / Num. obs: 16851 / % possible obs: 100 % / Redundancy: 4.8 % / CC1/2: 0.969 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.066 / Rrim(I) all: 0.147 / Net I/σ(I): 8
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
2.3-2.384.90.383810416480.8930.1920.433.7100
8.91-46.854.70.10714503100.9810.0540.1213.798.4

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1z57

1z57


Resolution: 2.3→46.9 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.887 / SU B: 13.594 / SU ML: 0.178 / SU R Cruickshank DPI: 0.3773 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.377 / ESU R Free: 0.263
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2578 782 4.6 %RANDOM
Rwork0.1805 ---
obs0.1841 16068 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 78.24 Å2 / Biso mean: 23.657 Å2 / Biso min: 8.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0.33 Å2
2---0.51 Å20 Å2
3---0.65 Å2
Refinement stepCycle: final / Resolution: 2.3→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 17 233 2994
Biso mean--15.63 28.69 -
Num. residues----338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132905
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172656
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.6393942
X-RAY DIFFRACTIONr_angle_other_deg1.3151.5866164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4165351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54321.925161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58715509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1741519
X-RAY DIFFRACTIONr_chiral_restr0.0830.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023328
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02637
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 51 -
Rwork0.209 1189 -
all-1240 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: 17.551 Å / Origin y: 4.882 Å / Origin z: 13.277 Å
111213212223313233
T0.0523 Å20.0102 Å2-0.0088 Å2-0.0518 Å20.0246 Å2--0.0168 Å2
L0.8863 °20.1112 °2-0.7966 °2-1.0042 °20.5072 °2--1.5782 °2
S-0.0105 Å °0.0947 Å °0.0559 Å °-0.1802 Å °-0.0241 Å °0.0141 Å °-0.1408 Å °0.0093 Å °0.0346 Å °

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