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- PDB-6qas: Crystal structure of ULK1 in complexed with PF-03814735 -

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Basic information

Entry
Database: PDB / ID: 6qas
TitleCrystal structure of ULK1 in complexed with PF-03814735
ComponentsSerine/threonine-protein kinase ULK1
KeywordsTRANSFERASE / ULK1 / autophagy / ATG1 / kinase / inhibitor complex / 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 / cellular response to stress / Macroautophagy / autophagosome membrane / autophagosome assembly / regulation of macroautophagy / cellular response to nutrient levels / negative regulation of protein-containing complex assembly / 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 / negative regulation of cell population proliferation / axon / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-34W / CITRIC ACID / Serine/threonine-protein kinase ULK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChaikuad, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Biochem.J. / Year: 2019
Title: Conservation of structure, function and inhibitor binding in UNC-51-like kinase 1 and 2 (ULK1/2).
Authors: Chaikuad, A. / Koschade, S.E. / Stolz, A. / Zivkovic, K. / Pohl, C. / Shaid, S. / Ren, H. / Lambert, L.J. / Cosford, N.D.P. / Brandts, C.H. / Knapp, S.
History
DepositionDec 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code_mod
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.4Oct 15, 2025Group: Structure summary / Category: audit_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,94236
Polymers64,8002
Non-polymers4,14234
Water6,936385
1
A: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,34219
Polymers32,4001
Non-polymers1,94218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,60017
Polymers32,4001
Non-polymers2,20016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.241, 74.241, 222.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 8 - 279 / Label seq-ID: 12 - 283

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 32400.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ULK1, KIAA0722 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-pRARE2
References: UniProt: O75385, non-specific serine/threonine protein kinase

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Non-polymers , 6 types, 419 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-34W / N-{2-[(1S,4R)-6-{[4-(cyclobutylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}-1,2,3,4-tetrahydro-1,4-epiminonaphthalen-9-yl]-2-oxoethyl}acetamide


Mass: 474.479 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H25F3N6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 2.8 M Ammonium sulfate, 0.1 M citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→47.47 Å / Num. obs: 63838 / % possible obs: 100 % / Redundancy: 9.2 % / Biso Wilson estimate: 23 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.4
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 6154 / CC1/2: 0.806 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WNO

4wno


Resolution: 1.75→47.47 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.975 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19651 3177 5 %RANDOM
Rwork0.17013 ---
obs0.17146 60554 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å2-0 Å2-0 Å2
2--0.41 Å2-0 Å2
3----0.83 Å2
Refine analyzeLuzzati coordinate error obs: 0.206 Å
Refinement stepCycle: 1 / Resolution: 1.75→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4375 0 272 385 5032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134804
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174535
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.6446477
X-RAY DIFFRACTIONr_angle_other_deg1.4141.59910523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44521.75240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25915834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8791532
X-RAY DIFFRACTIONr_chiral_restr0.0940.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025413
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02987
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_it1.6882.162224
X-RAY DIFFRACTIONr_mcbond_other1.6652.1522220
X-RAY DIFFRACTIONr_mcangle_it2.5493.2252783
X-RAY DIFFRACTIONr_mcangle_other2.5293.2222781
X-RAY DIFFRACTIONr_scbond_it2.8592.6882580
X-RAY DIFFRACTIONr_scbond_other2.8592.692581
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4113.8553678
X-RAY DIFFRACTIONr_long_range_B_refined6.52927.2895331
X-RAY DIFFRACTIONr_long_range_B_other6.52827.3025332
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8645 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 231 -
Rwork0.291 4347 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4036-0.0063-0.12780.4959-0.12640.5849-0.0375-0.05860.034-0.01370.0423-0.11170.06990.0717-0.00480.01350.0149-0.00120.0365-0.03960.0733-13.498629.359842.0557
20.94240.131-0.50540.40750.02121.00080.0308-0.04380.2177-0.03590.022-0.0378-0.05730.026-0.05280.0094-0.00240.00360.0069-0.02570.1082-20.525448.31535.8917
30.1567-0.1104-0.11761.46960.40660.58910.0168-0.0177-0.04250.03430.10060.1264-0.10770.0182-0.11740.0410.00450.02240.03090.01740.108312.537346.065646.6265
40.47510.24440.16930.56740.35320.48470.0256-0.0325-0.0413-0.0846-0.02280.0032-0.013-0.0155-0.00280.04750.0075-0.0420.0133-0.01730.069119.810626.004337.3058
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 152
2X-RAY DIFFRACTION2A153 - 281
3X-RAY DIFFRACTION3B8 - 108
4X-RAY DIFFRACTION4B109 - 280

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