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- PDB-5x8i: Crystal structure of human CLK1 in complex with compound 25 -

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Basic information

Entry
Database: PDB / ID: 5x8i
TitleCrystal structure of human CLK1 in complex with compound 25
ComponentsDual specificity protein kinase CLK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / Complex / Kinase / CLK1 / TRANSFERASE-TRANSFERASE INHIBITOR complex
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-SQZ / Dual specificity protein kinase CLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
AuthorsSun, Q.Z. / Lin, G.F. / Li, L.L. / Jin, X.T. / Huang, L.Y. / Zhang, G. / Wei, Y.Q. / Lu, G.W. / Yang, S.Y.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Discovery of Potent and Selective Inhibitors of Cdc2-Like Kinase 1 (CLK1) as a New Class of Autophagy Inducers
Authors: Sun, Q.Z. / Lin, G.F. / Li, L.L. / Jin, X.T. / Huang, L.Y. / Zhang, G. / Yang, W. / Chen, K. / Xiang, R. / Chen, C. / Wei, Y.Q. / Lu, G.W. / Yang, S.Y.
History
DepositionMar 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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
B: Dual specificity protein kinase CLK1
A: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9504
Polymers81,1312
Non-polymers8192
Water11,349630
1
B: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9752
Polymers40,5661
Non-polymers4091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9752
Polymers40,5661
Non-polymers4091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.330, 68.330, 285.721
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 40565.570 Da / Num. of mol.: 2 / Fragment: UNP residues 148-484 / Mutation: R432A
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-SQZ / 5-[1-[(1S)-1-(4-fluorophenyl)ethyl]-[1,2,3]triazolo[4,5-c]quinolin-8-yl]-1,3-benzoxazole / (S)-5-(1-(1-(4-fluorophenyl)ethyl)-1H-[1,2,3]triazolo[4,5-c]quinolin-8-yl)benzo[d]oxazole


Mass: 409.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H16FN5O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 2% (v/v) PEG 200, 20% (v/v) tacsimate (pH 7.0), 0.1M HEPES (pH 9.0)

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97849 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 58842 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.9 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 30.72
Reflection shellResolution: 1.9→1.97 Å / % possible obs: 100 % / Redundancy: 15.9 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 8.07 / Num. unique all: 5864 / CC1/2: 0.994 / Rsym value: 0.431

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VAG

2vag


Resolution: 1.902→33.6 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2064 2900 4.94 %
Rwork0.1661 --
obs0.1681 58718 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.902→33.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5386 0 62 630 6078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075598
X-RAY DIFFRACTIONf_angle_d1.1297575
X-RAY DIFFRACTIONf_dihedral_angle_d15.9023313
X-RAY DIFFRACTIONf_chiral_restr0.057810
X-RAY DIFFRACTIONf_plane_restr0.006959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9017-1.93290.20811080.18452638X-RAY DIFFRACTION99
1.9329-1.96620.25721490.1862670X-RAY DIFFRACTION100
1.9662-2.00190.2421650.18312631X-RAY DIFFRACTION100
2.0019-2.04040.23441430.17842657X-RAY DIFFRACTION100
2.0404-2.08210.24751500.17192648X-RAY DIFFRACTION100
2.0821-2.12730.24351540.17632666X-RAY DIFFRACTION100
2.1273-2.17680.20861370.16822641X-RAY DIFFRACTION100
2.1768-2.23130.19911710.16362650X-RAY DIFFRACTION100
2.2313-2.29160.19821220.16222669X-RAY DIFFRACTION100
2.2916-2.3590.22221090.16882708X-RAY DIFFRACTION100
2.359-2.43510.24231460.16962661X-RAY DIFFRACTION100
2.4351-2.52210.22281380.16942676X-RAY DIFFRACTION100
2.5221-2.6230.23361580.17052640X-RAY DIFFRACTION100
2.623-2.74240.19691340.17292668X-RAY DIFFRACTION100
2.7424-2.88690.21161270.16922659X-RAY DIFFRACTION100
2.8869-3.06760.21111150.16482690X-RAY DIFFRACTION100
3.0676-3.30430.15681320.16162674X-RAY DIFFRACTION100
3.3043-3.63650.1811240.1552688X-RAY DIFFRACTION100
3.6365-4.16190.19111270.14572670X-RAY DIFFRACTION100
4.1619-5.24030.18181380.152676X-RAY DIFFRACTION99
5.2403-33.60480.20491530.19422538X-RAY DIFFRACTION95

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