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- PDB-3sw4: Crystal Structure of the CDK2 in complex with thiazolylpyrimidine... -

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Basic information

Entry
Database: PDB / ID: 3sw4
TitleCrystal Structure of the CDK2 in complex with thiazolylpyrimidine inhibitor
ComponentsCyclin-dependent kinase 2
KeywordsTRANSFERASE/TRANSFERASE inhibitor / Alpha and beta protein (a+b) / 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 / 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 / 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 / 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-18K / ACETATE ION / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsKang, Y.N. / Stuckey, J.A.
CitationJournal: To be Published
Title: Crystal Structure of the CDK2 in complex with a thiazolylpyrimidine inhibitor
Authors: Kang, Y.N. / Stuckey, J.A.
History
DepositionJul 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Other
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 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_ref_seq_dif / 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_ref_seq_dif.details / _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: Cyclin-dependent kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3883
Polymers34,0031
Non-polymers3852
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.477, 72.144, 72.342
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Cyclin-dependent kinase 2 / 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 / Plasmid: pFB1 / Cell line (production host): High-five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P24941, cyclin-dependent kinase
#2: Chemical ChemComp-18K / N'-[4-(2-amino-4-methyl-1,3-thiazol-5-yl)pyrimidin-2-yl]-N,N-dimethylbenzene-1,4-diamine


Mass: 326.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N6S
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.05 Å3/Da / Density % sol: 40.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 15-20% PEG3350, 0.2M Ammonium Acetate, 0.1M HEPES pH 7.8, vapor diffusion, sitting drop, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2009 / Details: mirrors
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 37677 / Num. obs: 37564 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.048 / Χ2: 1.537 / Net I/σ(I): 14.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.6360.39117770.843196.6
1.63-1.666.30.34918340.941199.5
1.66-1.696.70.32818460.964199.8
1.69-1.7270.27418811.0261100
1.72-1.767.20.25718541.073199.9
1.76-1.87.30.21918591.1211100
1.8-1.857.30.19818631.2011100
1.85-1.97.30.15918671.4361100
1.9-1.957.30.13818571.6571100
1.95-2.027.30.11818631.9241100
2.02-2.097.30.1118751.8961100
2.09-2.177.20.09318622.0471100
2.17-2.277.20.08118871.7691100
2.27-2.397.30.06918701.9561100
2.39-2.547.20.06518871.7171100
2.54-2.747.10.0618961.8221100
2.74-3.017.10.05319191.7681100
3.01-3.457.20.04319151.552199.9
3.45-4.3470.03619291.774199.8
4.34-506.60.03120231.912197.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTBUSTER 2.11.1refinement
PDB_EXTRACT3.1data extraction
MD2data collection
HKL-2000data reduction
HKL-2000data scaling
BUSTER2.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→29.9 Å / Cor.coef. Fo:Fc: 0.9537 / Cor.coef. Fo:Fc free: 0.9433 / Occupancy max: 1 / Occupancy min: 0.4 / SU R Cruickshank DPI: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 1576 5.02 %RANDOM
Rwork0.1839 ---
obs0.1851 31405 99.86 %-
all-31449 --
Displacement parametersBiso max: 120.67 Å2 / Biso mean: 26.5265 Å2 / Biso min: 7.78 Å2
Baniso -1Baniso -2Baniso -3
1-1.029 Å20 Å20 Å2
2---1.5947 Å20 Å2
3---0.5657 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 27 143 2418
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1134SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes386HARMONIC5
X-RAY DIFFRACTIONt_it2428HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion308SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2929SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2428HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3312HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.51
X-RAY DIFFRACTIONt_other_torsion2.9
LS refinement shellResolution: 1.7→1.76 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.1999 155 5.48 %
Rwork0.1934 2674 -
all0.1938 2829 -
obs--99.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.80730.0355-0.01220.0098-0.32320-0.0001-0.01160.01960.01230.0145-0.0139-0.00260.0242-0.0144-0.0605-0.0008-0.0241-0.01030.04830.046418.755516.4321-11.9482
21.10720.41810.21551.525-0.06680.3401-0.0130.05570.1084-0.0712-0.0097-0.0584-0.03360.08780.0227-0.0302-0.00280.0132-0.04330.0255-0.006913.75022.5064-17.5381
31.3811-0.54060.52831.4956-0.41920.77720.0225-0.0805-0.07960.10240.01120.09320.00060.0341-0.0337-0.0183-0.00460.0003-0.04980.0007-0.03777.3395-14.9287-9.666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 34}A1 - 34
2X-RAY DIFFRACTION2{A|35 - 153}A35 - 153
3X-RAY DIFFRACTION3{A|164 - 298}A164 - 298

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