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- PDB-7ra5: CDK2 IN COMPLEX WITH COMPOUND 4 -

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Basic information

Entry
Database: PDB / ID: 7ra5
TitleCDK2 IN COMPLEX WITH COMPOUND 4
ComponentsCyclin-dependent kinase 2
KeywordsTRANSFERASE/INHIBITOR / CDK2 / CYCLIN-DEPENDENT KINASE 2 / PROTEROS BIOSTRUCTURES GMBH / TRANSFERASE / TRANSFERASE-INHIBITOR complex
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 / cyclin-dependent protein kinase activity / Y chromosome / 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 / cyclin-dependent protein kinase activity / Y chromosome / 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 / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / cellular response to nitric oxide / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Cajal body / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / 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 / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / : / meiotic cell cycle / positive regulation of DNA replication / male germ cell nucleus / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Meiotic recombination / Orc1 removal from chromatin / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / DNA replication / Ras protein signal transduction / transcription regulator complex / chromosome, telomeric region / endosome / chromatin remodeling / protein domain specific binding / cell division / protein phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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-3I3 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsMarineau, J.J. / Malojcic, G.
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery of SY-5609: A Selective, Noncovalent Inhibitor of CDK7.
Authors: Marineau, J.J. / Hamman, K.B. / Hu, S. / Alnemy, S. / Mihalich, J. / Kabro, A. / Whitmore, K.M. / Winter, D.K. / Roy, S. / Ciblat, S. / Ke, N. / Savinainen, A. / Wilsily, A. / Malojcic, G. / ...Authors: Marineau, J.J. / Hamman, K.B. / Hu, S. / Alnemy, S. / Mihalich, J. / Kabro, A. / Whitmore, K.M. / Winter, D.K. / Roy, S. / Ciblat, S. / Ke, N. / Savinainen, A. / Wilsily, A. / Malojcic, G. / Zahler, R. / Schmidt, D. / Bradley, M.J. / Waters, N.J. / Chuaqui, C.
History
DepositionJun 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: 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 / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: 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)34,5442
Polymers34,1051
Non-polymers4391
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14130 Å2
Unit cell
Length a, b, c (Å)53.615, 72.272, 70.818
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: 34104.621 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN
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-3I3 / 4-[7-(methanesulfonyl)-1H-indol-3-yl]-N-[(3S)-piperidin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine


Mass: 439.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20F3N5O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.05 Å3/Da / Density % sol: 39.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: PEG3350, MES pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.67→50.58 Å / Num. obs: 31991 / % possible obs: 98.1 % / Redundancy: 4.5 % / Biso Wilson estimate: 29.121 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.115 / Χ2: 0.95 / Net I/σ(I): 11.64
Reflection shellResolution: 1.67→1.92 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.932 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 123 / CC1/2: 1 / Rrim(I) all: 1.049 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
REFMAC5.8.0049phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PROPRIETARY MODEL

Resolution: 1.67→50.58 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.75 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2739 3270 10.3 %RANDOM
Rwork0.2252 ---
obs0.2302 28484 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.4 Å2 / Biso mean: 28.64 Å2 / Biso min: 10.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å2-0 Å20 Å2
2---1.34 Å20 Å2
3---2.33 Å2
Refinement stepCycle: final / Resolution: 1.67→50.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 30 171 2429
Biso mean--26.13 34.73 -
Num. residues----278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192288
X-RAY DIFFRACTIONr_bond_other_d0.0030.022198
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9883118
X-RAY DIFFRACTIONr_angle_other_deg0.99735042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8665281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.33823.47892
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92315372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9261512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212544
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02516
LS refinement shellResolution: 1.67→1.713 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 257 -
Rwork0.378 2111 -
all-2368 -
obs--98.79 %

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