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- PDB-2c5v: Differential Binding Of Inhibitors To Active And Inactive Cdk2 Pr... -

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Basic information

Entry
Database: PDB / ID: 2c5v
TitleDifferential Binding Of Inhibitors To Active And Inactive Cdk2 Provides Insights For Drug Design
Components
  • ALA-ALA-ABA-ARG-SER-LEU-ILE-PFF-NH2
  • CELL DIVISION PROTEIN KINASE 2
  • CYCLIN A2
KeywordsCELL CYCLE / ATP-BINDING / CELL DIVISION / COMPLEX (KINASE-CYCLIN) / CYCIN A / CYCLIN / DRUG DESIGN / LIGAND EXCHANGE / KINASE / MITOSIS / NUCLEOTIDE-BINDING / PHOSPHORYLATION / SERINE/THREONINE-PROTEIN KINASE / TRANSFERASE / COMPLEX (TRANSFERASE-CYCLIN)
Function / homology
Function and homology information


cellular response to luteinizing hormone stimulus / cellular response to cocaine / cell cycle G1/S phase transition / mitotic cell cycle phase transition / male pronucleus / female pronucleus / cellular response to insulin-like growth factor stimulus / cellular response to leptin stimulus / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity ...cellular response to luteinizing hormone stimulus / cellular response to cocaine / cell cycle G1/S phase transition / mitotic cell cycle phase transition / male pronucleus / female pronucleus / cellular response to insulin-like growth factor stimulus / cellular response to leptin stimulus / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity / cochlea development / cellular response to platelet-derived growth factor stimulus / regulation of DNA replication / regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin A1-CDK2 complex / cyclin E1-CDK2 complex / cyclin E2-CDK2 complex / positive regulation of DNA-dependent DNA replication initiation / cyclin A2-CDK2 complex / Y chromosome / cyclin-dependent protein kinase activity / X chromosome / histone phosphorylation / centrosome duplication / centriole replication / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / condensed chromosome / cyclin-dependent protein kinase holoenzyme complex / Cajal body / cellular response to nitric oxide / mitotic G1 DNA damage checkpoint / cyclin binding / regulation of gene silencing / potassium ion transport / meiotic cell cycle / cellular response to estradiol stimulus / chromosome, telomeric region / animal organ regeneration / G1/S transition of mitotic cell cycle / positive regulation of fibroblast proliferation / anaphase-promoting complex-dependent catabolic process / regulation of G2/M transition of mitotic cell cycle / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cellular response to hypoxia / Ras protein signal transduction / G2/M transition of mitotic cell cycle / transcription factor complex / regulation of signal transduction by p53 class mediator / DNA replication / endosome / peptidyl-serine phosphorylation / protein deubiquitination / centrosome / cell division / DNA repair / protein domain specific binding / protein serine/threonine kinase activity / protein phosphorylation / viral process / positive regulation of cell population proliferation / protein kinase binding / positive regulation of transcription, DNA-templated / negative regulation of transcription by RNA polymerase II / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Protein kinase-like domain superfamily / Cyclin-A, N-terminal / Protein kinase domain / Cyclin, C-terminal domain / Cyclin, N-terminal / Serine/threonine-protein kinase, active site / Protein kinase, ATP binding site / Cyclin-like / Cyclin-like superfamily / Cyclin ...Protein kinase-like domain superfamily / Cyclin-A, N-terminal / Protein kinase domain / Cyclin, C-terminal domain / Cyclin, N-terminal / Serine/threonine-protein kinase, active site / Protein kinase, ATP binding site / Cyclin-like / Cyclin-like superfamily / Cyclin / Protein kinase domain / Cyclin, N-terminal domain / Cyclin, C-terminal domain / Cyclin-like / Cyclin A; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Cyclin-dependent kinase 2 / Cyclin-A2
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKontopidis, G. / McInnes, C. / Pandalaneni, S.R. / McNae, I. / Gibson, D. / Mezna, M. / Thomas, M. / Wood, G. / Wang, S. / Walkinshaw, M.D. / Fischer, P.M.
CitationJournal: Chem.Biol. / Year: 2006
Title: Differential Binding of Inhibitors to Active and Inactive Cdk2 Provides Insights for Drug Design.
Authors: Kontopidis, G. / Mcinnes, C. / Pandalaneni, S.R. / Mcnae, I. / Gibson, D. / Mezna, M. / Thomas, M. / Wood, G. / Wang, S. / Walkinshaw, M.D. / Fischer, P.M.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 2, 2005Deposition site: PDBE / Processing site: PDBE
SupersessionMar 1, 2006ID: 1OKU
Revision 1.0Mar 1, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance

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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
B: CYCLIN A2
C: CELL DIVISION PROTEIN KINASE 2
D: CYCLIN A2
F: ALA-ALA-ABA-ARG-SER-LEU-ILE-PFF-NH2
H: ALA-ALA-ABA-ARG-SER-LEU-ILE-PFF-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,9198
Polymers129,2186
Non-polymers7012
Water3,387188
1
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A2
F: ALA-ALA-ABA-ARG-SER-LEU-ILE-PFF-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9594
Polymers64,6093
Non-polymers3501
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CELL DIVISION PROTEIN KINASE 2
D: CYCLIN A2
H: ALA-ALA-ABA-ARG-SER-LEU-ILE-PFF-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9594
Polymers64,6093
Non-polymers3501
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)74.501, 114.549, 156.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDAuth asym-IDAuth seq-ID
11A1 - 296
21C1 - 296
12B175 - 432
22D175 - 432

NCS ensembles:
ID
1
2

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Components

#1: Protein/peptide CELL DIVISION PROTEIN KINASE 2 / / CYCLIN-DEPENDENT KINASE 2 / P33 PROTEIN KINASE


Mass: 33976.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P24941, EC: 2.7.1.37
#2: Protein/peptide CYCLIN A2 / / CYCLIN A


Mass: 29753.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P20248
#3: Protein/peptide ALA-ALA-ABA-ARG-SER-LEU-ILE-PFF-NH2


Mass: 879.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical ChemComp-CK4 / 4-(2,4-DIMETHYL-1,3-THIAZOL-5-YL)-N-[4-(TRIFLUOROMETHYL)PHENYL]PYRIMIDIN-2-AMINE / 4-(2,4-DIMETHYL-THIAZOL-5-YL)-PYRIMIDIN-2-YL]-(4-TRIFLUOROMETHYL-PHENYL)-AMINE


Mass: 350.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13F3N4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 7.8 / Details: 22% PEG 3350, 0.1M NA3-CIT, pH 7.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 18, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.9→12 Å / Num. obs: 24322 / % possible obs: 84.5 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.7
Reflection shellResolution: 2.9→2.97 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.4 / % possible all: 86.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FIN
Resolution: 2.9→10 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.859 / SU B: 18.751 / SU ML: 0.351 / Cross valid method: THROUGHOUT / ESU R Free: 0.545 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1022 4.1 %RANDOM
Rwork0.171 ---
Obs0.175 24033 84.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.76 Å2
Baniso -1Baniso -2Baniso -3
1--3.98 Å20 Å20 Å2
2--0.7 Å20 Å2
3---3.27 Å2
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9047 0 48 188 9283
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0110.0229329
r_bond_other_d0.0010.028533
r_angle_refined_deg1.7751.99612671
r_angle_other_deg0.774319902
r_dihedral_angle_1_deg9.5251104
r_dihedral_angle_2_deg43.80723.924395
r_dihedral_angle_3_deg24.275151619
r_dihedral_angle_4_deg24.311545
r_chiral_restr0.0930.21432
r_gen_planes_refined0.0190.0210051
r_gen_planes_other0.0070.021828
r_nbd_refined0.3120.33085
r_nbd_other0.2950.39971
r_nbtor_refined0.2280.54785
r_nbtor_other0.1160.55295
r_xyhbond_nbd_refined0.2550.5630
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined0.360.329
r_symmetry_vdw_other0.4150.372
r_symmetry_hbond_refined0.4990.58
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it4.1241.56938
r_mcbond_other
r_mcangle_it5.28529047
r_mcangle_other
r_scbond_it7.88934564
r_scbond_other
r_scangle_it11.2294.53624
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refinement-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1740tight positional0.150.07
2B1523tight positional0.170.07
1A2898medium positional0.40.7
2B2513medium positional0.470.7
1A1740tight thermal0.60.9
2B1523tight thermal0.570.9
1A2898medium thermal1.592.3
2B2513medium thermal1.622.3
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.482 72
Rwork0.288 1708

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