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- PDB-6fdz: Unc-51-Like Kinase 3 (ULK3) In Complex With Momelotinib -

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Basic information

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


ciliary tip / fibroblast activation / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / positive regulation of smoothened signaling pathway / phagophore assembly site / reticulophagy / smoothened signaling pathway / response to starvation / autophagosome assembly ...ciliary tip / fibroblast activation / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / positive regulation of smoothened signaling pathway / phagophore assembly site / reticulophagy / smoothened signaling pathway / response to starvation / autophagosome assembly / mitophagy / autophagosome / negative regulation of smoothened signaling pathway / Hedgehog 'on' state / autophagy / cellular senescence / protein autophosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / regulation of autophagy / 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 / 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 kinase Atg1-like / MIT (microtubule interacting and transport) domain / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule domain / 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
Momelotinib / Serine/threonine-protein kinase ULK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMathea, S. / Salah, E. / Moroglu, M. / Scorah, A. / Pike, A.C.W. / 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 Momelotinib
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
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
U: Serine/threonine-protein kinase ULK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3542
Polymers31,9401
Non-polymers4141
Water1267
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 area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.836, 75.836, 214.691
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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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-C87 / Momelotinib


Mass: 414.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22N6O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, anticancer, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 0.2 M MgCl2, 30% 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.55→214.69 Å / Num. obs: 12814 / % possible obs: 100 % / Redundancy: 18.7 % / Rrim(I) all: 0.14 / Net I/σ(I): 17
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 19.7 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 608 / Rrim(I) all: 1.636 / % possible all: 100

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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: 2.55→65.68 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.897 / SU B: 10.806 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.435 / ESU R Free: 0.321 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30109 606 4.8 %RANDOM
Rwork0.23043 ---
obs0.23379 12141 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.642 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20.7 Å2-0 Å2
2--1.41 Å20 Å2
3----4.57 Å2
Refinement stepCycle: 1 / Resolution: 2.55→65.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 31 7 2067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192113
X-RAY DIFFRACTIONr_bond_other_d0.0020.021950
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.9592871
X-RAY DIFFRACTIONr_angle_other_deg1.0134482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2555263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12423.2181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65415332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9941511
X-RAY DIFFRACTIONr_chiral_restr0.090.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212434
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02441
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_it4.8476.141058
X-RAY DIFFRACTIONr_mcbond_other4.8456.1391059
X-RAY DIFFRACTIONr_mcangle_it6.9269.1931319
X-RAY DIFFRACTIONr_mcangle_other6.9279.1991320
X-RAY DIFFRACTIONr_scbond_it4.8186.3181055
X-RAY DIFFRACTIONr_scbond_other4.8166.3181056
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9529.3811553
X-RAY DIFFRACTIONr_long_range_B_refined9.17972.1762278
X-RAY DIFFRACTIONr_long_range_B_other9.17772.1822279
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.545→2.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 40 -
Rwork0.295 876 -
obs--100 %

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