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- PDB-6u5l: Structure of human ULK4 in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 6u5l
TitleStructure of human ULK4 in complex with an inhibitor
ComponentsSerine/threonine-protein kinase ULK4
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / kinase / pseudokinase / TRANSFERASE / TRANSFERASE-TRANSFERASE Inhibitor complex
Function / homology
Function and homology information


regulation of protein kinase C signaling / regulation of p38MAPK cascade / regulation of neuron migration / regulation of neuron projection development / regulation of MAPK cascade / regulation of JNK cascade / microtubule cytoskeleton organization / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity ...regulation of protein kinase C signaling / regulation of p38MAPK cascade / regulation of neuron migration / regulation of neuron projection development / regulation of MAPK cascade / regulation of JNK cascade / microtubule cytoskeleton organization / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
Serine/threonine-protein kinase ULK4 / Armadillo-like helical / Armadillo-type fold / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-3RJ / DI(HYDROXYETHYL)ETHER / Serine/threonine-protein kinase ULK4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsKhamrui, S. / Lazarus, M.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)K22CA201103 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: High-Resolution Structure and Inhibition of the Schizophrenia-Linked Pseudokinase ULK4.
Authors: Khamrui, S. / Ung, P.M.U. / Secor, C. / Schlessinger, A. / Lazarus, M.B.
History
DepositionAug 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase ULK4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1917
Polymers32,3201
Non-polymers8716
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.421, 90.421, 188.956
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Serine/threonine-protein kinase ULK4 / Unc-51-like kinase 4


Mass: 32320.129 Da / Num. of mol.: 1 / Mutation: K172A, K173A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ULK4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q96C45, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-3RJ / N~2~-(1H-benzimidazol-6-yl)-N~4~-(5-cyclobutyl-1H-pyrazol-3-yl)quinazoline-2,4-diamine


Mass: 396.448 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20N8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.45 Å3/Da / Density % sol: 64.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.25 / Details: PEG 6000, Imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0331 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 23, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 1.75→39.15 Å / Num. obs: 46829 / % possible obs: 99.8 % / Redundancy: 15 % / Biso Wilson estimate: 25.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.043 / Rrim(I) all: 0.163 / Net I/σ(I): 11.7
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 15.5 % / Rmerge(I) obs: 3.065 / Num. unique obs: 2541 / CC1/2: 0.6 / Rpim(I) all: 0.812 / Rrim(I) all: 3.173 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.55 Å44.38 Å
Translation2.55 Å44.38 Å

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Processing

Software
NameVersionClassification
Aimless0.5.12data scaling
PHASER2.5.7phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WNP

4wnp


Resolution: 1.75→39.15 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.27
RfactorNum. reflection% reflection
Rfree0.2165 2380 5.1 %
Rwork0.191 --
obs0.1922 46667 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.98 Å2 / Biso mean: 45.8982 Å2 / Biso min: 18.9 Å2
Refinement stepCycle: final / Resolution: 1.75→39.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2205 0 123 156 2484
Biso mean--55.09 44.72 -
Num. residues----276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032349
X-RAY DIFFRACTIONf_angle_d0.7223175
X-RAY DIFFRACTIONf_chiral_restr0.044346
X-RAY DIFFRACTIONf_plane_restr0.004396
X-RAY DIFFRACTIONf_dihedral_angle_d12.9311402
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.75-1.78570.41460.36572538100
1.7857-1.82460.3641610.33632526100
1.8246-1.8670.32511440.31732556100
1.867-1.91370.32781210.28522578100
1.9137-1.96540.30691470.27212559100
1.9654-2.02330.2351250.23832558100
2.0233-2.08860.2541350.22682577100
2.0886-2.16320.23481370.20782584100
2.1632-2.24980.21721590.18282555100
2.2498-2.35220.20941140.1858257299
2.3522-2.47620.22171270.1849258799
2.4762-2.63130.19471330.18372628100
2.6313-2.83440.23231370.18742635100
2.8344-3.11960.21421630.18172619100
3.1196-3.57070.19791540.17472644100
3.5707-4.49770.17551210.1522269999
4.4977-39.150.18321560.173287299
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)
15.0959-2.37892.0054.4227-2.17386.252-0.11490.1102-0.25580.0648-0.00170.08750.53-0.03350.11240.35080.00850.01370.27590.03710.240526.852352.836781.2869
23.95442.4731-4.52514.2012-2.47836.2802-0.05860.1879-0.07740.0190.08530.06530.5628-0.25280.0340.2596-0.0163-0.02750.21310.05660.195427.207452.75885.9722
34.1198-0.25290.62293.5281.35465.4624-0.0258-0.1545-0.2020.0104-0.01030.09180.1519-0.61510.02120.2043-0.0617-0.01840.3190.09080.21215.190260.452392.0709
41.7595-0.08180.47282.4964-1.09822.9718-0.06340.19750.2359-0.2541-0.00290.07790.18240.05170.11080.2047-0.03660.02890.24810.05370.216422.701761.525290.0144
52.16430.64410.56131.8313-1.99676.8008-0.06190.1406-0.13560.0142-0.0913-0.21531.0260.5964-0.01020.44190.07170.02580.2028-0.00120.275728.422951.24998.0705
67.2955-2.92381.60882.8422-2.66286.63890.1192-0.0933-0.2421-0.0217-0.2404-0.54020.52270.98680.16990.27980.0353-0.02070.35590.03880.2933.334657.4401111.8146
75.9247-4.3185-1.03393.5398-0.69766.11390.12210.0613-0.4374-0.122-0.1670.37810.2022-0.28780.10050.1838-0.0313-0.0160.22770.04050.210321.161960.5944106.2568
86.831-3.72960.16076.68670.80085.4411-0.0688-0.1786-0.20380.04760.09120.05770.2485-0.04540.00980.204-0.03060.01770.2490.05570.185622.856560.464102.4658
93.7903-2.93791.96396.3184-4.08713.57110.2512-0.7083-0.3362-0.23190.211.18720.4098-1.6992-0.52450.2468-0.10780.01190.74810.14780.45415.669159.541399.0526
104.1398-2.2610.16284.3302-0.94994.0960.0013-0.1134-0.21980.34850.02860.25270.3252-0.3812-0.02830.2937-0.05770.03340.30590.05380.258218.89556.683116.2383
114.18091.66930.51753.53760.14264.41260.1577-0.3262-0.47960.62050.118-0.07270.8719-0.1676-0.16940.5681-0.0106-0.04640.34290.13770.292623.154449.3976122.7196
122.34441.2329-1.32165.9979-0.72325.17530.0441-0.51930.34110.79860.0222-0.2482-0.39380.365-0.08660.4001-0.0399-0.05550.3229-0.00640.243927.085265.5997121.9111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -1:12)A-1 - 12
2X-RAY DIFFRACTION2(chain A and resid 13:34)A13 - 34
3X-RAY DIFFRACTION3(chain A and resid 35:54)A35 - 54
4X-RAY DIFFRACTION4(chain A and resid 55:73)A55 - 73
5X-RAY DIFFRACTION5(chain A and resid 74:91)A74 - 91
6X-RAY DIFFRACTION6(chain A and resid 92:114)A92 - 114
7X-RAY DIFFRACTION7(chain A and resid 115:129)A115 - 129
8X-RAY DIFFRACTION8(chain A and resid 130:151)A130 - 151
9X-RAY DIFFRACTION9(chain A and resid 152:185)A152 - 185
10X-RAY DIFFRACTION10(chain A and resid 186:218)A186 - 218
11X-RAY DIFFRACTION11(chain A and resid 219:263)A219 - 263
12X-RAY DIFFRACTION12(chain A and resid 264:285)A264 - 285

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