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- PDB-2r3p: Crystal Structure of Cyclin-Dependent Kinase 2 with inhibitor -

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Basic information

Entry
Database: PDB / ID: 2r3p
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 / G0 and Early G1 / Telomere Extension By Telomerase / 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 / 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) / 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-3SC / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.66 Å
AuthorsFischmann, T.O. / Hruza, A.W. / Madison, V.M. / Duca, J.S.
CitationJournal: Biopolymers / Year: 2008
Title: Structure-guided discovery of cyclin-dependent kinase inhibitors.
Authors: Fischmann, T.O. / Hruza, A. / Duca, J.S. / Ramanathan, L. / Mayhood, T. / Windsor, W.T. / Le, H.V. / Guzi, T.J. / Dwyer, M.P. / Paruch, K. / Doll, R.J. / Lees, E. / Parry, D. / Seghezzi, W. / Madison, V.
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 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4622
Polymers34,0351
Non-polymers4271
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.250, 71.290, 71.930
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: 34034.527 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-3SC / 5-(2,3-dichlorophenyl)-N-(pyridin-4-ylmethyl)-3-thiocyanatopyrazolo[1,5-a]pyrimidin-7-amine


Mass: 427.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H12Cl2N6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 38.72 %
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: Nov 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: 1.66→50 Å / Num. obs: 27720 / % possible obs: 84.7 % / Rmerge(I) obs: 0.032 / Χ2: 0.939 / Net I/σ(I): 22.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.67-1.680.4775640.93172.7
1.68-1.70.3985700.94570.3
1.7-1.710.3665910.86370.5
1.71-1.730.4065750.98674
1.73-1.750.3115740.92670.5
1.75-1.760.315810.96772.4
1.76-1.780.2615701.05471.2
1.78-1.80.2615800.97472.4
1.8-1.820.2426100.97375.6
1.82-1.840.2086030.93773.5
1.84-1.860.1956010.93376.1
1.86-1.880.1596270.93777.3
1.88-1.90.1426431.00478.4
1.9-1.930.136301.03179.9
1.93-1.950.0986860.85383.9
1.95-1.980.0877050.87486.9
1.98-2.010.0847200.96888.9
2.01-2.040.0747150.91687.8
2.04-2.070.0717320.90990.9
2.07-2.10.067390.84792.5
2.1-2.140.0617580.96291.9
2.14-2.180.0577280.88791.1
2.18-2.220.0527500.86891.6
2.22-2.270.0537230.93790
2.27-2.320.0467490.82790.5
2.32-2.370.0447380.98392.1
2.37-2.430.0437690.93491.8
2.43-2.490.0417400.89391.6
2.49-2.570.0357570.97192.3
2.57-2.650.0347540.93592.3
2.65-2.750.0337630.93993.5
2.75-2.860.037640.93992.4
2.86-2.990.0267660.84291.8
2.99-3.140.0247590.77991.8
3.14-3.340.0247630.8392.5
3.34-3.60.0247800.84692.4
3.6-3.960.0257590.9592
3.96-4.530.0267651.08589.3
4.53-5.710.0267681.22289
5.71-500.0277511.19680.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT2data extraction
BUSTER-TNTrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.66→36.7 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BUSTER-TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1402 -RANDOM
Rwork0.185 ---
all0.187 32775 --
obs0.187 27532 84 %-
Displacement parametersBiso mean: 31.329 Å2
Refinement stepCycle: LAST / Resolution: 1.66→36.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 56 238 2682

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