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- PDB-5vc5: Crystal structure of human WEE1 kinase domain in complex with PD-... -

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Basic information

Entry
Database: PDB / ID: 5vc5
TitleCrystal structure of human WEE1 kinase domain in complex with PD-166285
ComponentsWee1-like protein kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / KINASE DOMAIN / CELL CYCLE / WEE1 / TRANSFERASE / INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


G2/M DNA replication checkpoint / negative regulation of G2/M transition of mitotic cell cycle / Polo-like kinase mediated events / negative regulation of G1/S transition of mitotic cell cycle / establishment of cell polarity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / neuron projection morphogenesis ...G2/M DNA replication checkpoint / negative regulation of G2/M transition of mitotic cell cycle / Polo-like kinase mediated events / negative regulation of G1/S transition of mitotic cell cycle / establishment of cell polarity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / neuron projection morphogenesis / positive regulation of DNA replication / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / microtubule cytoskeleton organization / G2/M transition of mitotic cell cycle / Factors involved in megakaryocyte development and platelet production / protein tyrosine kinase activity / cell division / nucleolus / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Wee1-like protein kinase / : / 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 ...Wee1-like protein kinase / : / 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-96M / DI(HYDROXYETHYL)ETHER / Wee1-like protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsZhu, J.-Y. / Schonbrunn, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)UO1 HD076542 United States
CitationJournal: J. Med. Chem. / Year: 2017
Title: Structural Basis of Wee Kinases Functionality and Inactivation by Diverse Small Molecule Inhibitors.
Authors: Zhu, J.Y. / Cuellar, R.A. / Berndt, N. / Lee, H.E. / Olesen, S.H. / Martin, M.P. / Jensen, J.T. / Georg, G.I. / Schonbrunn, E.
History
DepositionMar 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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: Wee1-like protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1926
Polymers32,4411
Non-polymers7525
Water1,51384
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)50.530, 44.400, 61.980
Angle α, β, γ (deg.)90.000, 99.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Wee1-like protein kinase / WEE1hu / Wee1A kinase


Mass: 32440.900 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 291-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WEE1 / Plasmid: pET28a / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-RIPL
References: UniProt: P30291, non-specific protein-tyrosine kinase

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Non-polymers , 5 types, 89 molecules

#2: Chemical ChemComp-96M / 6-(2,6-dichlorophenyl)-2-({4-[2-(diethylamino)ethoxy]phenyl}amino)-8-methylpyrido[2,3-d]pyrimidin-7(8H)-one


Mass: 512.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H27Cl2N5O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 9.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 7.5 % PEG 3350, 1 mM PD-166285

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 15, 2016
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→35.907 Å / Num. obs: 20256 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 2.736 % / Biso Wilson estimate: 28.08 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.028 / Rrim(I) all: 0.034 / Χ2: 0.961 / Net I/σ(I): 25.07
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.93-1.982.720.313.6514750.9060.3899.2
1.98-2.032.7270.2215.0414600.9410.27199.2
2.03-2.092.7240.1836.0914220.9660.22599.2
2.09-2.162.7490.1377.8213630.9780.16898.9
2.16-2.232.7290.1189.213580.9830.14599
2.23-2.312.730.09410.9412960.9880.11598.9
2.31-2.392.7540.07713.4812410.9930.09498.6
2.39-2.492.7390.06615.6112060.9940.0899.2
2.49-2.62.730.05817.5911500.9950.0798.6
2.6-2.732.7530.04521.910780.9970.05598.7
2.73-2.882.7610.03626.7510530.9980.04498
2.88-3.052.7370.02933.769930.9990.03698.1
3.05-3.262.7210.02141.759180.9990.02696.9
3.26-3.522.7460.01751.58700.9990.02198.2
3.52-3.862.7540.01459.278060.9990.01898.1
3.86-4.322.7280.01365.3271710.01697.4
4.32-4.982.7270.01370.746520.9990.01698.8
4.98-6.12.7560.01366.4455010.01696.2
6.1-8.632.7360.01270.2141710.01595.9
8.63-35.9072.6190.01179.7623110.01490.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SERGUIdata collection
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V5Y

5v5y


Resolution: 1.93→35.907 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.71
RfactorNum. reflection% reflection
Rfree0.2169 1013 5 %
Rwork0.1763 --
obs-20255 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.71 Å2 / Biso mean: 47.1873 Å2 / Biso min: 16.8 Å2
Refinement stepCycle: final / Resolution: 1.93→35.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 91 84 2252
Biso mean--42.82 38.64 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122182
X-RAY DIFFRACTIONf_angle_d1.3682943
X-RAY DIFFRACTIONf_chiral_restr0.057315
X-RAY DIFFRACTIONf_plane_restr0.007376
X-RAY DIFFRACTIONf_dihedral_angle_d15.78814
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9299-2.03170.29611430.20452731287499
2.0317-2.1590.25191440.18562732287699
2.159-2.32560.22921460.17342760290699
2.3256-2.55960.21891440.17292744288899
2.5596-2.92980.25651450.18252754289999
2.9298-3.69070.19831440.17692734287898
3.6907-35.91290.19291470.16272787293497
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)
14.76261.3922-1.06474.5523-1.42263.4233-0.41440.3956-0.4738-0.57730.1828-0.13410.4653-0.14620.02230.3277-0.0127-0.00160.22840.04090.2736-12.7477-2.75989.1243
25.4996-2.3235-2.21172.70381.90863.22980.03250.4269-0.6041-0.7208-0.07790.02110.15840.00360.09810.46170.03460.07120.2201-0.0280.3068-2.9935-7.3036.2982
33.83271.05850.22542.2970.03091.44820.03190.0256-0.3713-0.2531-0.098-0.06260.26960.040.08560.34940.07190.04470.20590.0470.2317-1.0727-5.603714.8224
42.8106-0.8657-0.36314.2051-0.37412.67160.0996-0.18220.49580.2885-0.193-0.004-0.55650.09520.05020.3153-0.01450.00930.3013-0.00940.23983.683114.592820.5327
52.8242-0.71120.9164.4635-1.04343.52150.13060.173-0.13690.0161-0.539-0.17990.13050.21170.17230.27740.03940.00090.30220.04970.21178.17753.1516.3672
62.4789-1.3373-0.57343.0405-0.44350.95610.2326-0.24920.68130.0794-0.5648-1.0391-0.30290.7154-0.03660.3298-0.1059-0.06550.61050.17670.481618.115413.883919.3719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 293 through 323 )A293 - 323
2X-RAY DIFFRACTION2chain 'A' and (resid 324 through 337 )A324 - 337
3X-RAY DIFFRACTION3chain 'A' and (resid 338 through 383 )A338 - 383
4X-RAY DIFFRACTION4chain 'A' and (resid 384 through 420 )A384 - 420
5X-RAY DIFFRACTION5chain 'A' and (resid 421 through 484 )A421 - 484
6X-RAY DIFFRACTION6chain 'A' and (resid 485 through 571 )A485 - 571

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