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- PDB-2r3g: Crystal Structure of Cyclin-Dependent Kinase 2 with inhibitor -

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Basic information

Entry
Database: PDB / ID: 2r3g
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 / 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 / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cajal body / 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 / 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 / Transcriptional regulation of granulopoiesis / Orc1 removal from chromatin / 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 / cytosol / cytoplasm
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-SC9 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 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 30, 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

Downloads & links

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Assembly

Deposited unit
A: Cell division protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3222
Polymers34,0031
Non-polymers3191
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.010, 70.850, 71.780
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-SC9 / 6-(2-fluorophenyl)-N-(pyridin-3-ylmethyl)imidazo[1,2-a]pyrazin-8-amine


Mass: 319.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14FN5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 1.98 Å3/Da / Density % sol: 37.99 %
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: Aug 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: 1.55→50 Å / Num. obs: 39400 / % possible obs: 99.2 % / Rmerge(I) obs: 0.043 / Χ2: 0.928 / Net I/σ(I): 14.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.55-1.560.5129890.955100
1.56-1.580.4669590.992100
1.58-1.590.4479870.948100
1.59-1.610.4249850.955100
1.61-1.620.3759820.999100
1.62-1.640.3469470.968100
1.64-1.650.30110180.909100
1.65-1.670.2869490.937100
1.67-1.690.2729560.959100
1.69-1.710.25910220.953100
1.71-1.730.2319581.02100
1.73-1.750.2119780.963100
1.75-1.770.1929810.955100
1.77-1.790.1689760.975100
1.79-1.810.1539820.891100
1.81-1.840.1469990.905100
1.84-1.860.1169760.875100
1.86-1.890.1039990.862100
1.89-1.920.0979570.98799.9
1.92-1.950.0829770.8899.9
1.95-1.990.07210020.837100
1.99-2.020.0669930.867100
2.02-2.060.0639840.917100
2.06-2.10.0599790.883100
2.1-2.150.059920.854100
2.15-2.20.0489800.858100
2.2-2.250.0489920.971100
2.25-2.320.04310080.889100
2.32-2.380.049850.975100
2.38-2.460.0389941100
2.46-2.550.03610020.961100
2.55-2.650.03310060.893100
2.65-2.770.03110030.923100
2.77-2.920.0279850.8699.9
2.92-3.10.02710150.90599.8
3.1-3.340.02510080.89799.1
3.34-3.680.0249990.91998.8
3.68-4.210.0249950.94695.9
4.21-5.30.0249750.94393.4
5.3-500.0249260.93982.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT2data extraction
BUSTER-TNTrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.55→22.7 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber / Details: BUSTER-TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2008 -RANDOM
Rwork0.178 ---
all0.182 39770 --
obs0.182 39343 98.9 %-
Displacement parametersBiso mean: 25.511 Å2
Refinement stepCycle: LAST / Resolution: 1.55→22.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 27 269 2677

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