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- PDB-7s7a: Crystal structure of CDK2 liganded with compound EF3019 -

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Basic information

Entry
Database: PDB / ID: 7s7a
TitleCrystal structure of CDK2 liganded with compound EF3019
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-8FI / Uncharacterized protein
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: J.Med.Chem. / Year: 2023
Title: Screening through Lead Optimization of High Affinity, Allosteric Cyclin-Dependent Kinase 2 (CDK2) Inhibitors as Male Contraceptives That Reduce Sperm Counts in Mice.
Authors: Faber, E.B. / Wang, N. / John, K. / Sun, L. / Wong, H.L. / Burban, D. / Francis, R. / Tian, D. / Hong, K.H. / Yang, A. / Wang, L. / Elsaid, M. / Khalid, H. / Levinson, N.M. / Schonbrunn, E. ...Authors: Faber, E.B. / Wang, N. / John, K. / Sun, L. / Wong, H.L. / Burban, D. / Francis, R. / Tian, D. / Hong, K.H. / Yang, A. / Wang, L. / Elsaid, M. / Khalid, H. / Levinson, N.M. / Schonbrunn, E. / Hawkinson, J.E. / Georg, G.I.
History
DepositionSep 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 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
Revision 1.2Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)34,5125
Polymers33,9761
Non-polymers5364
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.920, 72.170, 72.530
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-8FI / 2-{[2-(2H-indazol-3-yl)ethyl]amino}-5-(trifluoromethyl)benzoic acid


Mass: 349.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C17H14F3N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 4.5mg/mL CDK2 protein crystalized under 25mM Na/K phosphate, 25mM Hepes Na, pH 7.5, 5% v/v PEG3350 was soaked overnight with 5mM EF3109 in 50mM Hepes Na, pH 7.5, 10% v/v PEG3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→27.77 Å / Num. obs: 31791 / % possible obs: 99.69 % / Redundancy: 3.3 % / Biso Wilson estimate: 28.56 Å2 / Rrim(I) all: 0.045 / Net I/σ(I): 21.14
Reflection shell
Resolution (Å)Num. unique obsRrim(I) allDiffraction-ID
7.6-27.714090.0251
5.38-7.66980.0261
4.39-5.386990.0241
3.8-4.3910160.0271
3.4-3.811590.0291
3.1-3.412630.0331
2.87-3.113940.041
2.69-2.8714460.0471
2.53-2.6915740.0541
2.4-2.5316290.0661
2.29-2.417430.0771
2.19-2.2917830.11
2.11-2.1918760.1081
2.03-2.1119350.1481
1.96-2.0319990.1781
1.9-1.9620880.251
1.84-1.921420.3691
1.79-1.8421850.5111
1.74-1.7922640.6191
1.7-1.7422990.8181

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4kd1

4kd1


Resolution: 1.7→27.77 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2383 1585 5 %
Rwork0.2058 30137 -
obs0.2075 31722 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.61 Å2 / Biso mean: 36.0614 Å2 / Biso min: 18.03 Å2
Refinement stepCycle: final / Resolution: 1.7→27.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 37 115 2337
Biso mean--42.77 38.01 -
Num. residues----278
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.750.38771400.33612678281899
1.75-1.820.30671410.2772671281299
1.82-1.890.30441410.248526962837100
1.89-1.980.29021430.224727082851100
1.98-2.080.27421430.225627122855100
2.08-2.210.27611420.215627252867100
2.21-2.380.2571440.220427292873100
2.38-2.620.26241450.217427472892100
2.62-30.25191460.219827712917100
3-3.780.21781460.202227822928100
3.78-27.770.19931540.173929183072100

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