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- PDB-2r3r: Crystal Structure of Cyclin-Dependent Kinase 2 with inhibitor -

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Basic information

Entry
Database: PDB / ID: 2r3r
TitleCrystal Structure of Cyclin-Dependent Kinase 2 with inhibitor
ComponentsCell division protein kinase 2
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / CELL CYCLE / INHIBITION / CYCLIN-DEPENDENT KINASE / CANCER / ATP-binding / Cell division / Mitosis / Nucleotide-binding / Phosphorylation / Polymorphism
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 / telomere maintenance in response to DNA damage / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / cellular response to nitric oxide / 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 / 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 / Cajal body / Cyclin A/B1/B2 associated events during G2/M transition / cyclin-dependent protein kinase holoenzyme complex / mitotic G1 DNA damage checkpoint signaling / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / regulation of G2/M transition of mitotic cell cycle / regulation of mitotic cell cycle / post-translational protein modification / cyclin binding / positive regulation of DNA replication / male germ cell nucleus / meiotic cell cycle / 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 / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / 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 / Senescence-Associated Secretory Phenotype (SASP) / peptidyl-serine phosphorylation / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / DNA replication / chromosome, telomeric region / endosome / chromatin remodeling / protein phosphorylation / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / 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
: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 ...: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-6SC / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.47 Å
AuthorsFischmann, T.O. / Hruza, A.W. / Madison, V.M. / Duca, J.S.
Citation
#1: Journal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Versatile templates for the development of novel kinase inhibitors: Discovery of novel CDK inhibitors.
Authors: Dwyer, M.P. / Paruch, K. / Alvarez, C. / Doll, R.J. / Keertikar, K. / Duca, J. / Fischmann, T.O. / Hruza, A. / Madison, V. / Lees, E. / Parry, D. / Seghezzi, W. / Sgambellone, N. / Shanahan, ...Authors: Dwyer, M.P. / Paruch, K. / Alvarez, C. / Doll, R.J. / Keertikar, K. / Duca, J. / Fischmann, T.O. / Hruza, A. / Madison, V. / Lees, E. / Parry, D. / Seghezzi, W. / Sgambellone, N. / Shanahan, F. / Wiswell, D. / Guzi, T.J.
History
DepositionAug 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 28, 2021Group: Derived calculations / Refinement description / Category: refine / struct_conn / struct_site
Item: _refine.ls_percent_reflns_obs / _struct_conn.pdbx_leaving_atom_flag ..._refine.ls_percent_reflns_obs / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3832
Polymers34,0031
Non-polymers3801
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.300, 71.320, 71.980
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 Cell division protein kinase 2 / p33 protein kinase


Mass: 34002.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2 / Production host: unidentified baculovirus / Strain (production host): SF9 / References: UniProt: P24941, cyclin-dependent kinase
#2: Chemical ChemComp-6SC / 3-bromo-5-phenyl-N-(pyridin-4-ylmethyl)pyrazolo[1,5-a]pyrimidin-7-amine


Mass: 380.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14BrN5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.4
Details: 50 mM Na-HEPES pH 7.4, 50 mM Ammonium Acetate, 8% PEG 4000, 4% Glycerol, 1 mM TCEP, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 1, 2002
RadiationMonochromator: Si(III) double crystal system / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 46918 / % possible obs: 99.7 % / Rmerge(I) obs: 0.034 / Χ2: 1.055 / Net I/σ(I): 20.8
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.47-1.480.45811381.03295.8
1.48-1.50.41511121.00599.7
1.5-1.510.38711751.045100
1.51-1.520.40111601.122100
1.52-1.540.33911361.052100
1.54-1.550.31711521.04100
1.55-1.570.29411801.026100
1.57-1.580.28411621.012100
1.58-1.60.24511531.052100
1.6-1.620.22411651.013100
1.62-1.640.2111471.042100
1.64-1.660.1911821.027100
1.66-1.680.1711421.053100
1.68-1.70.15911431.029100
1.7-1.720.14811941.055100
1.72-1.740.13311621.077100
1.74-1.770.11611701.002100
1.77-1.790.10311441.013100
1.79-1.820.09711761.018100
1.82-1.850.08411600.976100
1.85-1.880.07511740.994100
1.88-1.920.06811641.055100
1.92-1.960.05911711.025100
1.96-20.05211720.967100
2-2.040.04711791.023100
2.04-2.090.04811561.185100
2.09-2.140.04111911.023100
2.14-2.20.03811731.034100
2.2-2.260.03711611.158100
2.26-2.330.03212061.059100
2.33-2.420.03111741.018100
2.42-2.510.02911640.992100
2.51-2.630.02811921.133100
2.63-2.770.02611901.095100
2.77-2.940.02411871.035100
2.94-3.170.02312091.199.9
3.17-3.490.02212021.151100
3.49-3.990.02212131.11199.9
3.99-5.030.02112271.16399.7
5.03-500.02212601.16195

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT2data extraction
BUSTER-TNTrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.47→42.7 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BUSTER-TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2388 -RANDOM
Rwork0.187 ---
all0.188 47041 --
obs0.188 46839 99.6 %-
Displacement parametersBiso mean: 25.227 Å2
Refinement stepCycle: LAST / Resolution: 1.47→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2410 0 27 228 2665

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