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- PDB-9ob3: CDK2/CyclinE bound to compound 16 with P-loop in the EE conformation -

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Basic information

Entry
Database: PDB / ID: 9ob3
TitleCDK2/CyclinE bound to compound 16 with P-loop in the EE conformation
Components
  • Cyclin-dependent kinase 2
  • G1/S-specific cyclin-E1
KeywordsCELL CYCLE / CDK/Cyclin
Function / homology
Function and homology information


positive regulation of mesenchymal stem cell proliferation / homologous chromosome pairing at meiosis / RHOBTB3 ATPase cycle / cyclin-dependent protein serine/threonine kinase regulator activity / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase ...positive regulation of mesenchymal stem cell proliferation / homologous chromosome pairing at meiosis / RHOBTB3 ATPase cycle / cyclin-dependent protein serine/threonine kinase regulator activity / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / Y chromosome / cyclin-dependent protein kinase activity / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X chromosome / G1/S-Specific Transcription / PTK6 Regulates Cell Cycle / regulation of anaphase-promoting complex-dependent catabolic process / Association of TriC/CCT with target proteins during biosynthesis / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / telomere maintenance in response to DNA damage / microtubule organizing center / centrosome duplication / G0 and Early G1 / Telomere Extension By Telomerase / DNA replication initiation / Activation of the pre-replicative complex / positive regulation of G1/S transition of mitotic cell cycle / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cajal body / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Activation of ATR in response to replication stress / 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 / cyclin-dependent protein kinase holoenzyme complex / condensed chromosome / regulation of G2/M transition of mitotic cell cycle / mitotic G1 DNA damage checkpoint signaling / cellular response to nitric oxide / telomere maintenance / post-translational protein modification / cyclin binding / regulation of mitotic cell cycle / positive regulation of DNA replication / meiotic cell cycle / male germ cell nucleus / G1/S transition of mitotic cell cycle / peptidyl-serine phosphorylation / DNA Damage/Telomere Stress Induced Senescence / potassium ion transport / CDK-mediated phosphorylation and removal of Cdc6 / Meiotic recombination / SCF(Skp2)-mediated degradation of p27/p21 / G2/M transition of mitotic cell cycle / Wnt signaling pathway / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / kinase activity / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / regulation of protein localization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / transcription regulator complex / Regulation of TP53 Activity through Phosphorylation / Ras protein signal transduction / chromosome, telomeric region / DNA replication / protein phosphorylation / endosome / chromatin remodeling / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / positive regulation of cell population proliferation / DNA-templated transcription / centrosome / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma ...Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / 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
: / G1/S-specific cyclin-E1 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsBaird, J. / Holliday, M.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Nanoscale direct-to-biology optimization of Cdk2 inhibitors
Authors: Douthwaite, J.L. / Houde, D.J. / Pardo, E. / Moran, M.S. / Baird, J. / Meyer, S.R. / Mahjour, B. / Zhao, Q. / Larrow, J.F. / Juang, Y. / Han, C.K. / Kelley, B. / Dunstan, D.R. / Holliday, M. ...Authors: Douthwaite, J.L. / Houde, D.J. / Pardo, E. / Moran, M.S. / Baird, J. / Meyer, S.R. / Mahjour, B. / Zhao, Q. / Larrow, J.F. / Juang, Y. / Han, C.K. / Kelley, B. / Dunstan, D.R. / Holliday, M.J. / Billings, K.J. / Mader, M.M. / Taylor, A.M. / Sexton, J.Z. / Boezio, A.A. / Cernak, T.
History
DepositionApr 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclin-dependent kinase 2
B: G1/S-specific cyclin-E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8513
Polymers67,4662
Non-polymers3841
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-21 kcal/mol
Surface area24900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.160, 101.160, 151.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Cyclin-dependent kinase 2 / Cell division protein kinase 2 / p33 protein kinase


Mass: 34412.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24941, cyclin-dependent kinase
#2: Protein G1/S-specific cyclin-E1


Mass: 33053.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNE1, CCNE / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24864
#3: Chemical ChemComp-A1CAH / (1R,3R)-3-{3-[(pyrazine-2-carbonyl)amino]-1H-pyrazol-5-yl}cyclopentyl [(1S)-1-cyclopropylethyl]carbamate


Mass: 384.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24N6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.115 M Sodium Citrate, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11582 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11582 Å / Relative weight: 1
ReflectionResolution: 1.98→151.07 Å / Num. obs: 55305 / % possible obs: 100 % / Redundancy: 25.6 % / Biso Wilson estimate: 52.17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.019 / Rrim(I) all: 0.07 / Net I/σ(I): 25.3
Reflection shellResolution: 1.98→2.03 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3826 / CC1/2: 0.383

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→84.06 Å / SU ML: 0.2802 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4036
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.244 1999 3.62 %
Rwork0.219 53181 -
obs0.2199 55180 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.73 Å2
Refinement stepCycle: LAST / Resolution: 1.98→84.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4644 0 28 63 4735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00384793
X-RAY DIFFRACTIONf_angle_d0.64016508
X-RAY DIFFRACTIONf_chiral_restr0.0426730
X-RAY DIFFRACTIONf_plane_restr0.0046816
X-RAY DIFFRACTIONf_dihedral_angle_d13.48771768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.41091400.37233725X-RAY DIFFRACTION99.97
2.03-2.080.34931410.34833730X-RAY DIFFRACTION100
2.08-2.150.311400.2913752X-RAY DIFFRACTION99.97
2.15-2.220.28061400.27383752X-RAY DIFFRACTION99.97
2.22-2.290.37821400.34413706X-RAY DIFFRACTION99.07
2.29-2.390.28621420.26523771X-RAY DIFFRACTION100
2.39-2.490.28791410.24953752X-RAY DIFFRACTION99.97
2.49-2.630.29511410.24373766X-RAY DIFFRACTION100
2.63-2.790.26491430.25983782X-RAY DIFFRACTION100
2.79-3.010.30361430.27083798X-RAY DIFFRACTION100
3.01-3.310.2841430.24333831X-RAY DIFFRACTION99.97
3.31-3.790.23871440.21493836X-RAY DIFFRACTION99.97
3.79-4.770.18061470.18233896X-RAY DIFFRACTION100
4.77-84.060.22261540.18424084X-RAY DIFFRACTION99.88
Refinement TLS params.Method: refined / Origin x: 26.3029962247 Å / Origin y: 6.579577834 Å / Origin z: -18.6103776871 Å
111213212223313233
T0.29836651513 Å2-0.0356205616563 Å2-0.0236229832465 Å2-0.46222357115 Å2-0.0117880999931 Å2--0.398097583525 Å2
L1.22666325937 °20.256193870344 °20.772259246226 °2-1.8954381825 °20.898645252339 °2--2.81103887827 °2
S0.22351924713 Å °0.180962011127 Å °-0.149324280716 Å °6.78231780803E-5 Å °0.053305759679 Å °-0.110060794949 Å °0.383594355414 Å °0.309860002969 Å °-0.212894987255 Å °
Refinement TLS groupSelection details: all

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