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- PDB-6q8p: Structure of CLK1 with bound N-methyl-10-nitropyrido[3,4-g]quinaz... -

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Basic information

Entry
Database: PDB / ID: 6q8p
TitleStructure of CLK1 with bound N-methyl-10-nitropyrido[3,4-g]quinazolin-2-amine
ComponentsDual specificity protein kinase CLK1
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / TYROSINE-PROTEIN KINASE / NUCLEUS / INHIBITOR / 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 / phosphorylation / 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. / 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-HQB / : / Dual specificity protein kinase CLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJoerger, A.C. / Chatterjee, D. / Schroeder, M. / Tazarki, H. / Zeinyeh, W. / Esvan, Y.J. / Khiari, J. / Josselin, B. / Baratte, B. / Bach, S. ...Joerger, A.C. / Chatterjee, D. / Schroeder, M. / Tazarki, H. / Zeinyeh, W. / Esvan, Y.J. / Khiari, J. / Josselin, B. / Baratte, B. / Bach, S. / Ruchaud, S. / Anizon, F. / Giraud, F. / Moreau, P. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Eur J Med Chem / Year: 2019
Title: New pyrido[3,4-g]quinazoline derivatives as CLK1 and DYRK1A inhibitors: synthesis, biological evaluation and binding mode analysis.
Authors: Tazarki, H. / Zeinyeh, W. / Esvan, Y.J. / Knapp, S. / Chatterjee, D. / Schroder, M. / Joerger, A.C. / Khiari, J. / Josselin, B. / Baratte, B. / Bach, S. / Ruchaud, S. / Anizon, F. / Giraud, F. / Moreau, P.
History
DepositionDec 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 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
A: Dual specificity protein kinase CLK1
B: Dual specificity protein kinase CLK1
C: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,5497
Polymers118,7453
Non-polymers8054
Water1448
1
A: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8763
Polymers39,5821
Non-polymers2942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8372
Polymers39,5821
Non-polymers2551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8372
Polymers39,5821
Non-polymers2551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.791, 117.553, 91.911
Angle α, β, γ (deg.)90.00, 99.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 39581.512 Da / Num. of mol.: 3
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-HQB / ~{N}-methyl-10-nitro-pyrido[3,4-g]quinazolin-2-amine


Mass: 255.232 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H9N5O2
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein solution: 7-8 mg/ml protein in 30 mM Hepes, pH 7.5, 300 mM NaCl, 50 mM arginine/glutamine mix 1:1, 0.5 mM TCEP, and 1% v/v glycerol. Reservoir solution: 29% (v/v) 1,2 propanediol, 0. ...Details: Protein solution: 7-8 mg/ml protein in 30 mM Hepes, pH 7.5, 300 mM NaCl, 50 mM arginine/glutamine mix 1:1, 0.5 mM TCEP, and 1% v/v glycerol. Reservoir solution: 29% (v/v) 1,2 propanediol, 0.08 M Na/K phosphate. Crystals were soaked for 72 h in reservoir solution complemented with 1 mM compound and 20% 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 / Detector: PIXEL / Date: Oct 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3→47.1 Å / Num. obs: 23961 / % possible obs: 100 % / Redundancy: 3.5 % / CC1/2: 0.973 / Rmerge(I) obs: 0.162 / Net I/σ(I): 5.2
Reflection shellResolution: 3→3.18 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.683 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5v1j

5v1j


Resolution: 3→45.39 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 1185 4.96 %
Rwork0.1982 --
obs0.2005 23876 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7971 0 58 8 8037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058241
X-RAY DIFFRACTIONf_angle_d0.55711181
X-RAY DIFFRACTIONf_dihedral_angle_d14.3674904
X-RAY DIFFRACTIONf_chiral_restr0.0431234
X-RAY DIFFRACTIONf_plane_restr0.0041488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.13650.34371560.29642817X-RAY DIFFRACTION100
3.1365-3.30180.34621600.25272807X-RAY DIFFRACTION100
3.3018-3.50860.29231380.23342856X-RAY DIFFRACTION100
3.5086-3.77940.25861390.2052833X-RAY DIFFRACTION100
3.7794-4.15950.25271500.18632838X-RAY DIFFRACTION100
4.1595-4.76090.21841510.16152845X-RAY DIFFRACTION100
4.7609-5.9960.19041410.17422848X-RAY DIFFRACTION100
5.996-45.39540.19331500.18182847X-RAY DIFFRACTION98

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