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- PDB-9f32: Crystal structure of ULK1 with a covalent compound GCL 99 -

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Basic information

Entry
Database: PDB / ID: 9f32
TitleCrystal structure of ULK1 with a covalent compound GCL 99
ComponentsSerine/threonine-protein kinase ULK1
KeywordsTRANSFERASE / Kinase / Covalent / inhibitor / MAP2K6 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


neuron projection regeneration / omegasome membrane / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / positive regulation of autophagosome assembly / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs / regulation of tumor necrosis factor-mediated signaling pathway / phagophore assembly site ...neuron projection regeneration / omegasome membrane / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / positive regulation of autophagosome assembly / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs / regulation of tumor necrosis factor-mediated signaling pathway / phagophore assembly site / axon extension / TBC/RABGAPs / reticulophagy / Receptor Mediated Mitophagy / response to starvation / Macroautophagy / cellular response to stress / autophagosome membrane / autophagosome assembly / regulation of macroautophagy / negative regulation of protein-containing complex assembly / cellular response to nutrient levels / mitophagy / positive regulation of autophagy / autophagosome / macroautophagy / Regulation of TNFR1 signaling / recycling endosome / peptidyl-serine phosphorylation / small GTPase binding / autophagy / neuron projection development / intracellular protein localization / protein autophosphorylation / GTPase binding / mitochondrial outer membrane / protein phosphorylation / non-specific serine/threonine protein kinase / regulation of autophagy / axon / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein-containing complex binding / signal transduction / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Serine/threonine-protein kinase, Ulk1/Ulk2 / Serine/threonine-protein kinase Atg1-like, tMIT domain / : / Atg1-like, MIT domain 1 / ATG1-like, MIT domain 2 / Serine/threonine-protein kinase Atg1-like / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Serine/threonine-protein kinase, Ulk1/Ulk2 / Serine/threonine-protein kinase Atg1-like, tMIT domain / : / Atg1-like, MIT domain 1 / ATG1-like, MIT domain 2 / Serine/threonine-protein kinase Atg1-like / 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
Similarity search - Domain/homology
: / Serine/threonine-protein kinase ULK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, G.Q. / Seidler, N. / Gehringer, M. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
The Structural Genomics Consortium (SGC) Canada
Citation
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2018
Title: The Cysteinome of Protein Kinases as a Target in Drug Development.
Authors: Chaikuad, A. / Koch, P. / Laufer, S.A. / Knapp, S.
History
DepositionApr 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5082
Polymers32,2421
Non-polymers2651
Water72140
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 area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.921, 56.946, 115.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine/threonine-protein kinase ULK1 / Autophagy-related protein 1 homolog / ATG1 / hATG1 / Unc-51-like kinase 1


Mass: 32242.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ULK1, KIAA0722 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O75385, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1H9M / N-[4-(1H-indazol-5-yl)phenyl]propanamide / N-[4-(1H-indazol-5-yl)phenyl]prop-2-enamide (covalently bound)


Mass: 265.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG 10000---- 0.1M Sodium HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.1→43.92 Å / Num. obs: 17644 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.999 / Net I/σ(I): 14.8
Reflection shellResolution: 2.1→2.16 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1388 / CC1/2: 0.804

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→41.1 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.022 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25361 873 5 %RANDOM
Rwork0.22144 ---
obs0.22305 16717 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.634 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.69 Å2-0 Å2
3----0.79 Å2
Refinement stepCycle: 1 / Resolution: 2.1→41.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 20 40 1961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131969
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151883
X-RAY DIFFRACTIONr_angle_refined_deg1.651.642658
X-RAY DIFFRACTIONr_angle_other_deg1.3391.5834328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9495238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19121.845103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.315346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2481513
X-RAY DIFFRACTIONr_chiral_restr0.0740.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02455
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_it4.4994.776961
X-RAY DIFFRACTIONr_mcbond_other4.4964.775960
X-RAY DIFFRACTIONr_mcangle_it6.3547.1221196
X-RAY DIFFRACTIONr_mcangle_other6.3527.1241197
X-RAY DIFFRACTIONr_scbond_it5.4345.2511008
X-RAY DIFFRACTIONr_scbond_other5.4315.2521009
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9857.6511463
X-RAY DIFFRACTIONr_long_range_B_refined11.21189.4487974
X-RAY DIFFRACTIONr_long_range_B_other11.21489.4387963
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 62 -
Rwork0.249 1174 -
obs--100 %

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