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- PDB-6fdy: Unc-51-Like Kinase 3 (ULK3) In Complex With Bosutinib -

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Basic information

Entry
Database: PDB / ID: 6fdy
TitleUnc-51-Like Kinase 3 (ULK3) In Complex With Bosutinib
ComponentsSerine/threonine-protein kinase ULK3
KeywordsTRANSFERASE / Kinase Inhibitor DFG-in
Function / homology
Function and homology information


ciliary tip / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / fibroblast activation / positive regulation of smoothened signaling pathway / phagophore assembly site / reticulophagy / smoothened signaling pathway / response to starvation / autophagosome assembly ...ciliary tip / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / fibroblast activation / positive regulation of smoothened signaling pathway / phagophore assembly site / reticulophagy / smoothened signaling pathway / response to starvation / autophagosome assembly / autophagosome / negative regulation of smoothened signaling pathway / regulation of autophagy / Hedgehog 'on' state / autophagy / cellular senescence / protein autophosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase Atg1-like / MIT (microtubule interacting and transport) domain / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...Serine/threonine-protein kinase Atg1-like / MIT (microtubule interacting and transport) domain / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-DB8 / Serine/threonine-protein kinase ULK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMathea, S. / Salah, E. / Moroglu, M. / Scorah, A. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Huber, K. / Knapp, S.
CitationJournal: To Be Published
Title: Unc-51-Like Kinase 3 (ULK3) In Complex With Bosutinib
Authors: Mathea, S. / Salah, E. / Moroglu, M. / Scorah, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Huber, K. / Knapp, S.
History
DepositionDec 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
U: Serine/threonine-protein kinase ULK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0013
Polymers31,9401
Non-polymers1,0612
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.375, 169.406, 45.919
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein Serine/threonine-protein kinase ULK3 / Unc-51-like kinase 3


Mass: 31939.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ULK3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6PHR2, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-DB8 / 4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile / Bosutinib / Bosutinib


Mass: 530.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H29Cl2N5O3 / Comment: inhibitor, medication*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5; 0.2 M sodium citrate; 30% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.7→48.18 Å / Num. obs: 39968 / % possible obs: 100 % / Redundancy: 6.5 % / Rrim(I) all: 0.09 / Net I/σ(I): 13.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1951 / Rrim(I) all: 0.824 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wnp

4wnp


Resolution: 1.7→48.18 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.236 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23871 2010 5 %RANDOM
Rwork0.20521 ---
obs0.20686 37958 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.039 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å2-0 Å2
2--1.01 Å20 Å2
3----1.38 Å2
Refinement stepCycle: 1 / Resolution: 1.7→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 72 127 2247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192173
X-RAY DIFFRACTIONr_bond_other_d0.0020.021989
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.9332945
X-RAY DIFFRACTIONr_angle_other_deg1.1234590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1975259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92323.65693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20615355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0251513
X-RAY DIFFRACTIONr_chiral_restr0.1440.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212576
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02441
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3012.3421043
X-RAY DIFFRACTIONr_mcbond_other2.2892.3391042
X-RAY DIFFRACTIONr_mcangle_it3.1453.4981302
X-RAY DIFFRACTIONr_mcangle_other3.1443.4991302
X-RAY DIFFRACTIONr_scbond_it3.1582.6021130
X-RAY DIFFRACTIONr_scbond_other3.1572.6031131
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6683.7981644
X-RAY DIFFRACTIONr_long_range_B_refined5.51227.4442249
X-RAY DIFFRACTIONr_long_range_B_other5.49527.2932232
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.703→1.747 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 138 -
Rwork0.284 2773 -
obs--99.86 %

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