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- PDB-7n3u: Crystal structure of human WEE1 kinase domain in complex with ZN-c3 -

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Basic information

Entry
Database: PDB / ID: 7n3u
TitleCrystal structure of human WEE1 kinase domain in complex with ZN-c3
ComponentsWee1-like protein kinase
KeywordsTRANSFERASE / phosphotransferase / protein kinase-like / alpha and beta proteins (a+b) / cell division
Function / homology
Function and homology information


negative regulation of G2/MI transition of meiotic cell cycle / 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 ...negative regulation of G2/MI transition of meiotic cell cycle / 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 / phosphorylation / 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
Chem-05J / Wee1-like protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLee, C.C.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery of ZN-c3, a Highly Potent and Selective Wee1 Inhibitor Undergoing Evaluation in Clinical Trials for the Treatment of Cancer.
Authors: Huang, P.Q. / Boren, B.C. / Hegde, S.G. / Liu, H. / Unni, A.K. / Abraham, S. / Hopkins, C.D. / Paliwal, S. / Samatar, A.A. / Li, J. / Bunker, K.D.
History
DepositionJun 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Apr 13, 2022Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)32,6952
Polymers32,1691
Non-polymers5271
Water50428
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)45.920, 50.510, 119.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 32168.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WEE1 / Plasmid: pET21b / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): codon plus
References: UniProt: P30291, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-05J / 1-[(7R)-7-ethyl-7-hydroxy-6,7-dihydro-5H-cyclopenta[b]pyridin-2-yl]-6-[4-(4-methylpiperazin-1-yl)anilino]-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one


Mass: 526.633 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H34N8O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12723 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12723 Å / Relative weight: 1
ReflectionResolution: 2.65→46.57 Å / Num. obs: 8565 / % possible obs: 99.8 % / Redundancy: 10.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.027 / Rrim(I) all: 0.089 / Net I/σ(I): 17.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.65-2.7810.80.7831188510980.930.2470.8222.799.7
8.79-46.538.80.0425182870.9980.0130.04243.899.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V5Y

5v5y


Resolution: 2.65→46.53 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 39.736 / SU ML: 0.396 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2668 430 5 %RANDOM
Rwork0.2169 ---
obs0.2196 8095 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.18 Å2 / Biso mean: 71.916 Å2 / Biso min: 45.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å2-0 Å2-0 Å2
2---6.69 Å20 Å2
3---8.66 Å2
Refinement stepCycle: final / Resolution: 2.65→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 39 29 2147
Biso mean--57.98 64.19 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132167
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172023
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.6662930
X-RAY DIFFRACTIONr_angle_other_deg1.1261.5964684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0765259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93821.441118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.30415378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7791517
X-RAY DIFFRACTIONr_chiral_restr0.0490.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022406
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02466
LS refinement shellResolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 36 -
Rwork0.369 580 -
all-616 -
obs--99.35 %
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)
10.63640.17150.73315.92473.71083.03070.24770.18530.0067-0.1412-0.3558-0.25010.1963-0.14840.10810.1531-0.00570.16230.213-0.24190.592220.2339-17.6821-22.5563
20.52131.2548-0.77513.279-1.68291.64980.1434-0.0313-0.28310.4911-0.2646-0.7809-0.19780.12270.12110.2587-0.07380.03610.25930.01310.44324.6852-12.3186-21.5655
30.6563-0.6942-1.84921.0261.28458.4086-0.0283-0.01030.11790.04750.0848-0.28280.11920.3698-0.05640.1072-0.0414-0.01120.2548-0.0220.211826.73181.165-16.0557
41.267-1.0471-0.31574.18630.54140.10240.18450.3542-0.24530.3714-0.23310.0988-0.0041-0.08220.04860.2268-0.02950.03820.2208-0.11120.139912.0691-8.9284-16.5905
55.4782-0.11291.86344.15890.91960.85850.10070.137-0.22490.6103-0.0169-0.09470.20370.0271-0.08370.346-0.07230.07520.1433-0.03220.046211.93760.8118-9.9469
61.9275-1.1408-0.2133.1784-0.10970.052-0.02040.38820.16840.09970.0204-0.1631-0.007-0.1037-0.00010.2469-0.05330.0280.3455-0.03850.04487.254312.4884-18.0611
74.23092.2195-0.09126.1715-0.49270.0415-0.16490.39660.55251.4730.22950.9284-0.1352-0.0093-0.06460.4947-0.02010.18410.1758-0.04930.2305-0.298211.0507-7.3418
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A293 - 318
2X-RAY DIFFRACTION2A319 - 337
3X-RAY DIFFRACTION3A338 - 353
4X-RAY DIFFRACTION4A354 - 399
5X-RAY DIFFRACTION5A400 - 479
6X-RAY DIFFRACTION6A480 - 528
7X-RAY DIFFRACTION7A529 - 570

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