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- PDB-8fp0: Ternary complex of CDK2 with small molecule ligands TW8672 and Ro... -

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Basic information

Entry
Database: PDB / ID: 8fp0
TitleTernary complex of CDK2 with small molecule ligands TW8672 and Roscovitine
ComponentsCyclin-dependent kinase 2
KeywordsCell Cycle / Transferase / allosteric / inhibitor
Function / homology
Function and homology information


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 ...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 / PTK6 Regulates Cell Cycle / regulation of anaphase-promoting complex-dependent catabolic process / 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 / centrosome duplication / G0 and Early G1 / Telomere Extension By Telomerase / Activation of the pre-replicative complex / 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 / 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 / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / Meiotic recombination / SCF(Skp2)-mediated degradation of p27/p21 / G2/M transition of mitotic cell cycle / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / 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 / 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
: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 ...: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-7TW / R-ROSCOVITINE / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchonbrunn, E. / Sun, L.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Nat Commun / Year: 2023
Title: Development of allosteric and selective CDK2 inhibitors for contraception with negative cooperativity to cyclin binding.
Authors: Faber, E.B. / Sun, L. / Tang, J. / Roberts, E. / Ganeshkumar, S. / Wang, N. / Rasmussen, D. / Majumdar, A. / Hirsch, L.E. / John, K. / Yang, A. / Khalid, H. / Hawkinson, J.E. / Levinson, N.M. ...Authors: Faber, E.B. / Sun, L. / Tang, J. / Roberts, E. / Ganeshkumar, S. / Wang, N. / Rasmussen, D. / Majumdar, A. / Hirsch, L.E. / John, K. / Yang, A. / Khalid, H. / Hawkinson, J.E. / Levinson, N.M. / Chennathukuzhi, V. / Harki, D.A. / Schonbrunn, E. / Georg, G.I.
History
DepositionJan 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)34,7805
Polymers33,9761
Non-polymers8044
Water1,63991
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)53.820, 72.100, 72.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIPL / References: UniProt: P24941, cyclin-dependent kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-RRC / R-ROSCOVITINE


Mass: 354.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26N6O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-7TW / 2-{[2-(1H-indol-3-yl)ethyl]amino}-5-nitrobenzoic acid


Mass: 325.319 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15N3O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 3350, 20% ethylene glycol, 50mM HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.6→37.07 Å / Num. obs: 37459 / % possible obs: 98.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 29.5 Å2 / CC1/2: 1 / Rrim(I) all: 0.045 / Net I/σ(I): 17.7
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3.97 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2564 / CC1/2: 0.687 / Rrim(I) all: 0.992 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSJan 10, 2022data reduction
XSCALEJan 10, 2022data scaling
PHENIX1.20.1-4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RWF

7rwf


Resolution: 1.6→37.07 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2404 1872 5 %
Rwork0.2113 --
obs0.2127 37452 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→37.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2197 0 58 91 2346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.942
X-RAY DIFFRACTIONf_dihedral_angle_d9.141308
X-RAY DIFFRACTIONf_chiral_restr0.059350
X-RAY DIFFRACTIONf_plane_restr0.009393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.36551330.34842530X-RAY DIFFRACTION92
1.64-1.690.27821390.28222649X-RAY DIFFRACTION97
1.69-1.750.30711410.26462670X-RAY DIFFRACTION98
1.75-1.810.30131440.24662734X-RAY DIFFRACTION99
1.81-1.880.31741420.26922708X-RAY DIFFRACTION99
1.88-1.970.31921450.24122742X-RAY DIFFRACTION100
1.97-2.070.21861430.21622721X-RAY DIFFRACTION99
2.07-2.20.28921440.21252740X-RAY DIFFRACTION100
2.2-2.370.25191450.22252761X-RAY DIFFRACTION100
2.37-2.610.26281460.21432767X-RAY DIFFRACTION100
2.61-2.990.25021470.22482790X-RAY DIFFRACTION99
2.99-3.760.21471480.2012821X-RAY DIFFRACTION100
3.76-37.070.21391550.18882947X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.7761 Å / Origin y: 4.3721 Å / Origin z: 13.1666 Å
111213212223313233
T0.1774 Å20.0016 Å2-0.0049 Å2-0.2314 Å20.004 Å2--0.1972 Å2
L0.878 °20.0869 °2-0.3529 °2-3.3052 °2-0.2155 °2--1.0099 °2
S0.0406 Å °0.0218 Å °-0.1051 Å °-0.056 Å °-0.0407 Å °-0.2077 Å °0.0718 Å °0.1283 Å °-0.0068 Å °
Refinement TLS groupSelection details: all

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