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- PDB-5vd7: CRYSTAL STRUCTURE OF HUMAN WEE1 KINASE DOMAIN IN COMPLEX WITH RAC... -

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Basic information

Entry
Database: PDB / ID: 5vd7
TitleCRYSTAL STRUCTURE OF HUMAN WEE1 KINASE DOMAIN IN COMPLEX WITH RAC-IV-098, 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-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-99V / Wee1-like protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.08 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 1.2Oct 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)33,0574
Polymers32,4411
Non-polymers6163
Water1,26170
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)50.190, 44.550, 64.640
Angle α, β, γ (deg.)90.000, 102.050, 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-99V / 6-{[3-fluoro-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


Mass: 518.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31FN8O2
#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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
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-098

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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: Aug 17, 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: 2.08→32.988 Å / Num. obs: 16808 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.716 % / Biso Wilson estimate: 31.17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.053 / Χ2: 0.979 / Net I/σ(I): 17.79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.08-2.133.6730.3064.1512190.930.35897.1
2.13-2.193.6840.2315.3812180.9630.27199.4
2.19-2.263.6580.1976.1711530.9680.23198
2.26-2.333.6890.1687.1311430.9740.19698.8
2.33-2.43.7970.1378.7911010.9870.15998.7
2.4-2.493.8070.11710.4710690.9870.13698.8
2.49-2.583.8310.10511.6610280.9890.12299.3
2.58-2.693.8310.08214.3410040.9920.09698.7
2.69-2.83.7960.06916.179600.9940.0898.8
2.8-2.943.7980.0619.278990.9960.0799.4
2.94-3.13.7810.04922.778720.9970.05899.4
3.1-3.293.740.04126.088160.9970.04899.4
3.29-3.523.6580.03629.137860.9980.04298.9
3.52-3.83.6620.03233.027200.9980.03798.1
3.8-4.163.6220.0335.086660.9980.03699.1
4.16-4.653.5980.02837.366140.9980.03398.4
4.65-5.373.6850.02736.955310.9990.03299.3
5.37-6.583.5960.02836.564580.9980.03397.4
6.58-9.33.5040.02439.183550.9980.02996.7
9.3-32.9883.2240.02939.071960.9980.03592.9

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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: 2.08→32.988 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.55
RfactorNum. reflection% reflection
Rfree0.2479 840 5 %
Rwork0.2072 --
obs-16804 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.78 Å2 / Biso mean: 50.4459 Å2 / Biso min: 16.46 Å2
Refinement stepCycle: final / Resolution: 2.08→32.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 80 70 2227
Biso mean--42.24 35.68 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052166
X-RAY DIFFRACTIONf_angle_d0.8752926
X-RAY DIFFRACTIONf_chiral_restr0.033314
X-RAY DIFFRACTIONf_plane_restr0.003373
X-RAY DIFFRACTIONf_dihedral_angle_d16.257810
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0801-2.21040.3051380.24892627276598
2.2104-2.3810.32791400.23892652279299
2.381-2.62060.27251390.23332642278199
2.6206-2.99950.27141390.23442640277999
2.9995-3.77820.24021410.20182682282399
3.7782-32.99250.211430.17762721286498
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)
15.90720.7948-0.46085.05640.13385.1569-0.13870.0512-0.6195-0.3642-0.0195-0.04390.2212-0.31620.13070.28240.0042-0.00750.30140.08650.3873-11.507-2.38687.6337
24.1294-2.0167-1.15342.70160.91434.51340.0334-0.4319-0.6855-0.3460.12750.37820.24520.5449-0.05550.3620.0043-0.04670.280.06490.3471-7.2073-6.80569.4356
36.1413-0.14581.60041.3402-0.34426.530.12460.5179-1.3412-0.7573-0.32560.84850.1441-0.5037-0.30620.76450.0897-0.17570.2785-0.07660.61875.8176-9.475913.7773
44.31751.6350.94835.10250.54762.2611-0.0243-0.2825-0.1731-0.23150.03960.17230.26560.074-0.10120.20230.07020.04030.22170.09930.1546-5.0393-3.652715.5733
53.1589-0.5580.54332.979-0.97343.2314-0.2433-0.29630.47930.36390.0146-0.2195-0.6921-0.1135-0.01980.3340.0151-0.05020.2263-0.0140.19033.115611.705819.9955
64.14451.4519-0.03522.1427-1.26782.4820.13561.057-0.5589-0.6806-0.4325-0.62110.60520.28170.25380.41670.08590.07060.42880.11040.554613.7404-0.951613.4845
74.6918-0.75250.27414.1668-0.59242.0298-0.1733-0.10931.19290.4014-0.2736-1.1613-0.46430.4621-0.80660.3757-0.0562-0.16590.37250.11160.664917.950813.570718.962
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 383 )A354 - 383
5X-RAY DIFFRACTION5chain 'A' and (resid 384 through 461 )A384 - 461
6X-RAY DIFFRACTION6chain 'A' and (resid 462 through 484 )A462 - 484
7X-RAY DIFFRACTION7chain 'A' and (resid 485 through 571 )A485 - 571

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