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- PDB-7s9x: Crystal structure of CDK2 liganded with compound WN378 -

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Basic information

Entry
Database: PDB / ID: 7s9x
TitleCrystal structure of CDK2 liganded with compound WN378
ComponentsCyclin-dependent kinase 2
KeywordsCELL CYCLE / allosteric inhibitor / drug development / kinase
Function / homologyReplication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Chem-8KF / Uncharacterized protein
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsSun, L. / Schonbrunn, E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)1R61HD099743-01 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA076292 United States
CitationJournal: To Be Published
Title: Development of selective allosteric inhibitors of cyclin-dependent kinase 2 (CDK2)
Authors: Sun, L. / Schonbrunn, E.
History
DepositionSep 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

Deposited unit
A: Cyclin-dependent kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3472
Polymers33,9761
Non-polymers3701
Water30617
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)53.657, 71.924, 72.371
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 Cyclin-dependent kinase 2 / Cell division protein kinase 2 / p33 protein kinase


Mass: 33976.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, cyclin-dependent kinase
#2: Chemical ChemComp-8KF / 2-[(9H-carbazol-3-yl)amino]-5-(trifluoromethyl)benzoic acid


Mass: 370.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H13F3N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.06 Å3/Da / Density % sol: 40.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 4.5 mg/mL CDK2 crystalized in 50 mM sodium/potassium phosphate, 50 mM HEPES, pH 7.5, 5% v/v PEG3350, soaked overnight in 1 mM WN378 in 50 mM phosphate, 50 mM HEPES Na, 10% v/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.53→43.12 Å / Num. obs: 38877 / % possible obs: 90.25 % / Redundancy: 5.1 % / Biso Wilson estimate: 33.14 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.1 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
4.15-43.140.05166.722350.9950.057195.23
3.3-4.1547.422160.995199.95
2.88-3.32221820.9891
2.62-2.8813.821790.9821
2.43-2.6210.121480.9771
2.29-2.4321850.9691
2.17-2.29521390.9581
2.08-2.173.921360.9571
2-2.082.821170.9481
1.93-22.121480.9341
1.87-1.931.421480.911
1.81-1.870.921230.9521
1.77-1.810.620890.9291
1.72-1.770.519980.941
1.68-1.720.419070.921
1.65-1.680.318020.86784.64
1.62-1.650.216000.83675.12
1.58-1.620.213690.78664.64
1.56-1.580.111890.79855.8
1.53-1.560.19670.7545.87

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874_3874refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4dk1

4dk1


Resolution: 1.69→43.01 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2623 2072 3.46 %
Rwork0.2301 57770 -
obs0.2312 31807 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.95 Å2 / Biso mean: 43.4128 Å2 / Biso min: 24.59 Å2
Refinement stepCycle: final / Resolution: 1.69→43.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2137 0 27 17 2181
Biso mean--49.84 34.77 -
Num. residues----269
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.69-1.730.4351270.40943569369690
1.73-1.770.35471320.36883705383796
1.77-1.820.35751460.3133837398399
1.82-1.870.35111370.279139094046100
1.87-1.930.2681340.256738774011100
1.93-20.27791450.240839114056100
2-2.080.25371440.239638744018100
2.08-2.180.26541430.233738874030100
2.18-2.290.32441330.246538744007100
2.29-2.440.32571370.252139234060100
2.44-2.630.31171410.240838604001100
2.63-2.890.27921360.259539374073100
2.89-3.310.26241360.24633861399799
3.31-4.160.21811360.21238794015100
4.17-43.010.23241450.19123867401299

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