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- PDB-5vd8: Crystal structure of human WEE1 kinase domain in complex with RAC... -

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Basic information

Entry
Database: PDB / ID: 5vd8
TitleCrystal structure of human WEE1 kinase domain in complex with RAC-IV-099, a MK1775 analogue
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-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / 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 / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-98M / Wee1-like protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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: to be published
Title: Structural basis of Wee family kinase inhibition by small molecules
Authors: Zhu, J.-Y. / Schonbrunn, E.
History
DepositionApr 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 15, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
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)33,1365
Polymers32,4411
Non-polymers6954
Water1,22568
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)50.290, 44.560, 64.980
Angle α, β, γ (deg.)90.000, 101.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-98M / 6-{[3-chloro-4-(4-methylpiperazin-1-yl)phenyl]amino}-1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one / RAC-IV-099


Mass: 535.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31ClN8O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 5.0 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 RAC-IV-099

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 8, 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: 1.85→43.511 Å / Num. obs: 24209 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.669 % / Biso Wilson estimate: 28.9 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.088 / Χ2: 0.981 / Net I/σ(I): 11.96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.93.5990.2864.5817590.9350.33699.3
1.9-1.953.590.2215.6217380.9590.2699.1
1.95-2.013.570.186.6616750.9690.21299.5
2.01-2.073.5810.1437.7816180.9770.16899.7
2.07-2.143.5890.1218.7516030.9850.14399.4
2.14-2.213.6570.10610.0715230.9870.12599.5
2.21-2.293.7250.09411.1515040.9870.11100
2.29-2.393.7670.08612.3414460.9890.10199.7
2.39-2.493.7730.08113.3513680.990.09499.7
2.49-2.623.7660.07513.9113150.990.08799.9
2.62-2.763.7710.07315.0212330.9910.08599.4
2.76-2.933.740.06915.7812010.9920.08199.8
2.93-3.133.7440.06816.6511090.9890.07999.9
3.13-3.383.7360.06917.4110430.9890.08199.5
3.38-3.73.7260.06917.899620.9880.0899.9
3.7-4.143.7020.06918.28760.9860.081100
4.14-4.783.6770.06818.337720.9890.07998.7
4.78-5.853.6430.0718.096490.9880.08299.7
5.85-8.273.5320.07417.925260.9840.087100
8.27-43.5113.1830.0817.022890.9840.09797

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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: 1.85→43.511 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.22
RfactorNum. reflection% reflection
Rfree0.2469 1210 5 %
Rwork0.2033 --
obs-24205 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.93 Å2 / Biso mean: 49.6555 Å2 / Biso min: 15.29 Å2
Refinement stepCycle: final / Resolution: 1.85→43.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 90 68 2228
Biso mean--37.08 37.98 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072162
X-RAY DIFFRACTIONf_angle_d0.9062918
X-RAY DIFFRACTIONf_chiral_restr0.033312
X-RAY DIFFRACTIONf_plane_restr0.004372
X-RAY DIFFRACTIONf_dihedral_angle_d16.231809
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8499-1.9240.28311340.23612535266999
1.924-2.01160.28111330.22492531266499
2.0116-2.11760.30711330.22725222655100
2.1176-2.25030.23711330.224525452678100
2.2503-2.4240.30021330.217825282661100
2.424-2.66790.26791350.21825592694100
2.6679-3.05390.27551360.223125712707100
3.0539-3.84720.26351350.192225672702100
3.8472-43.52260.19761380.18022637277599
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)
15.62440.6245-0.98365.0693-0.40374.5987-0.33230.476-0.6339-0.60360.1086-0.04410.3902-0.19720.17690.32860.0035-0.01020.27460.05690.3323-11.527-2.11487.6536
22.86020.7184-0.80151.80791.09284.9468-0.3992-0.5423-1.0523-0.15990.42430.40080.65140.54060.06530.34520.01650.01050.1840.09790.3164-7.139-6.32489.6039
31.99040.38372.42333.16750.86442.9850.4430.3456-0.9929-0.73630.2940.44520.5132-0.2259-0.56940.72310.0406-0.06950.3245-0.02570.66676.0082-9.171413.6068
42.42251.2378-0.33861.128-0.50260.25840.3243-0.5581-0.51030.629-0.0944-0.28120.58720.0349-0.09260.28030.0426-0.01350.19780.11930.2397-3.8064-4.600619.653
54.41770.0068-0.0246.72641.1813.7208-0.2243-0.0301-0.4775-0.50310.23980.51430.38890.18220.03910.22990.0210.00870.17060.07030.1528-6.2406-2.019211.3953
67.53460.6112-1.29961.17360.66450.8573-0.04050.42281.4260.4404-0.12380.0403-1.4709-0.298-0.16540.78260.0718-0.09840.26090.02270.5016-0.679222.260912.742
73.12050.7540.23143.1298-0.35822.1862-0.2608-0.61020.33590.7236-0.0037-0.2926-0.316-0.01890.04220.33920.0403-0.03130.2623-0.00930.18084.81258.08822.7573
84.27440.51141.18562.6612-1.1632.98910.17070.905-0.4958-0.4752-0.4392-0.62020.54630.55790.29950.37480.11620.06920.46310.09570.410213.7799-0.627813.5531
94.7817-2.98060.17384.8423-0.29241.5038-0.1718-0.11360.31390.0214-0.1426-0.7643-0.050.4160.28970.2873-0.0095-0.02750.34090.12560.456918.68426.484916.9714
100.03910.21940.15922.83930.83960.71470.07450.84990.5777-1.4495-0.0987-0.669-0.46050.4134-0.16350.48150.06280.07240.64740.7210.903718.711816.64017.7035
110.8474-0.2953-0.31273.8371-1.73391.7713-0.4905-0.75221.31130.7088-0.1896-1.4399-0.61280.663-1.49350.568-0.1247-0.3760.4545-0.04680.761517.399517.109824.4792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 293 through 318 )A293 - 318
2X-RAY DIFFRACTION2chain 'A' and (resid 319 through 337 )A319 - 337
3X-RAY DIFFRACTION3chain 'A' and (resid 338 through 353 )A338 - 353
4X-RAY DIFFRACTION4chain 'A' and (resid 354 through 368 )A354 - 368
5X-RAY DIFFRACTION5chain 'A' and (resid 369 through 383 )A369 - 383
6X-RAY DIFFRACTION6chain 'A' and (resid 384 through 399 )A384 - 399
7X-RAY DIFFRACTION7chain 'A' and (resid 400 through 461 )A400 - 461
8X-RAY DIFFRACTION8chain 'A' and (resid 462 through 484 )A462 - 484
9X-RAY DIFFRACTION9chain 'A' and (resid 485 through 510 )A485 - 510
10X-RAY DIFFRACTION10chain 'A' and (resid 511 through 527 )A511 - 527
11X-RAY DIFFRACTION11chain 'A' and (resid 528 through 571 )A528 - 571

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