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- PDB-1jvp: Crystal structure of human CDK2 (unphosphorylated) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 1jvp
TitleCrystal structure of human CDK2 (unphosphorylated) in complex with PKF049-365
ComponentsCell division protein kinase 2
KeywordsTRANSFERASE / Protein Kinase / Cell Division / Cell cycle / Enzyme Inhibitors / Drug design
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 / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / Cajal body / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Activation of ATR in response to replication stress / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / 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 / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / meiotic cell cycle / male germ cell nucleus / response to organic substance / G1/S transition of mitotic cell cycle / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Meiotic recombination / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / 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) / regulation of gene expression / peptidyl-serine phosphorylation / Ras protein signal transduction / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / DNA replication / chromosome, telomeric region / endosome / chromatin remodeling / cell division / protein domain specific binding / protein phosphorylation / DNA repair / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / DNA-templated transcription / positive regulation of cell population proliferation / 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
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. ...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
3-pyridin-4-yl-2,4-dihydroindeno[1,2-c]pyrazole / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsRondeau, J.M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2002
Title: Structure-based design and protein X-ray analysis of a protein kinase inhibitor.
Authors: Furet, P. / Meyer, T. / Strauss, A. / Raccuglia, S. / Rondeau, J.M.
History
DepositionAug 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Sep 22, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 600HETEROGEN THERE ARE TWO TAUTOMERIC FORMS OF THE COMPOUND (LIG) WHICH CORRESPONDS TO THE TWO ...HETEROGEN THERE ARE TWO TAUTOMERIC FORMS OF THE COMPOUND (LIG) WHICH CORRESPONDS TO THE TWO ALTERNATE CONFROMATIONS LABELLED (1) AND (2), RESPECTIVELY, IN THE PDB FILE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: Cell division protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2102
Polymers33,9761
Non-polymers2331
Water4,756264
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.528, 71.802, 72.362
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: 33976.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): H5 (Trichoplusia ni) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24941, EC: 2.7.1.37
#2: Chemical ChemComp-89E / 3-pyridin-4-yl-2,4-dihydroindeno[1,2-c]pyrazole


Mass: 233.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11N3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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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 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 4000, sodium chloride, ammonium acetate, sodium azide, Hepes, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16.25 mg/mlprotein1drop
210 mMHEPES1drop
315 mM1droppH7.4NaCl
4100 mMHEPES1reservoirpH7.6
550 mMammonium acetate1reservoir
610 %PEG40001reservoir
70.02 %sodium azide1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 6, 1998
RadiationMonochromator: sagitally focused, channel-cut Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.53→30 Å / Num. all: 39979 / Num. obs: 39944 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 14
Reflection shellResolution: 1.53→1.62 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2 / Num. unique all: 4990 / % possible all: 75.4
Reflection
*PLUS
Num. measured all: 179814

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: two alternate conformations built for ligand and also for kinase residues 81 to 85 which make non-bonded contacts to the ligand
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3864 10.1 %RANDOM
Rwork0.206 ---
all0.215 38946 --
obs0.21 38298 89.5 %-
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.53→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2409 0 36 264 2709
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_improper_angle_d0.69
X-RAY DIFFRACTIONx_mcbond_it1.451.5
X-RAY DIFFRACTIONx_mcangle_it2.392
X-RAY DIFFRACTIONx_scbond_it2.332
X-RAY DIFFRACTIONx_scangle_it3.622.5
LS refinement shellResolution: 1.53→1.63 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 503 9.9 %
Rwork0.31 4573 -
obs--72.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
Refinement
*PLUS
Rfactor obs: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS

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