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- PDB-9d0r: Crystal structure of human Wee1 kinase domain in complex with inh... -

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Basic information

Entry
Database: PDB / ID: 9d0r
TitleCrystal structure of human Wee1 kinase domain in complex with inhibitor
ComponentsWee1-like protein kinase
KeywordsTRANSFERASE/INHIBITOR / tyrosine-protein kinase / kinase / transferase / inhibitor / complex / 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 / : / 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
Similarity search - Domain/homology
: / Wee1-like protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsBell, J.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Harnessing free energy calculations for kinome-wide selectivity in drug discovery campaigns with a Wee1 case study.
Authors: Knight, J.L. / Clark, A.J. / Wang, J. / Placzek, A. / Bos, P.H. / Bhat, S. / Bell, J.A. / Silvergleid, S. / Yin, W. / Gray, F. / Sun, S. / Akinsanya, K. / Abel, R. / Gerasyuto, A.I.
History
DepositionAug 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Wee1-like protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1328
Polymers32,4851
Non-polymers6477
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.571, 69.571, 157.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 32485.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WEE1 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P30291, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-A1A1T / 7-methyl-2-{[1-(1-methylpiperidin-4-yl)-1H-pyrazol-4-yl]amino}-6-[(1R)-1-(thiophen-2-yl)ethyl]-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile


Mass: 446.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26N8S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: hepes, sodium chloride, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.34→30 Å / Num. obs: 16942 / % possible obs: 99.1 % / Redundancy: 11.2 % / CC1/2: 0.987 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.055 / Rrim(I) all: 0.182 / Net I/σ(I): 9.5
Reflection shellResolution: 2.34→2.47 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2404 / CC1/2: 0.917 / Rpim(I) all: 0.22 / Rrim(I) all: 0.772 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PRIME-Xrefinement
MOSFLM7.3.0data reduction
SCALA3.3.22data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→29.01 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.256 837 5 %Random
Rwork0.214 ---
obs-16862 100 %-
Solvent computationBsol: 69.39 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 43.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.214 Å20 Å20 Å2
2---0.214 Å20 Å2
3---0.428 Å2
Refinement stepCycle: LAST / Resolution: 2.34→29.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 38 250 2389
Refine LS restraintsType: OPLS 2005X
LS refinement shellResolution: 2.34→2.43 Å
RfactorNum. reflection% reflection
Rfree0.322 84 5 %
Rwork0.28 1686 -
obs--100 %

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