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- PDB-4acm: CDK2 IN COMPLEX WITH 3-AMINO-6-(4-{[2-(DIMETHYLAMINO)ETHYL]SULFAM... -

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Basic information

Entry
Database: PDB / ID: 4acm
TitleCDK2 IN COMPLEX WITH 3-AMINO-6-(4-{[2-(DIMETHYLAMINO)ETHYL]SULFAMOYL}-PHENYL)-N-PYRIDIN-3-YLPYRAZINE-2-CARBOXAMIDE
ComponentsCYCLIN-DEPENDENT KINASE 2
KeywordsTRANSFERASE / MITOSIS / CELL CYCLE / SERINE/THREONINE- PROTEIN KINASE / ATP-BINDING / CELL DIVISION / NUCLEOTIDE-BINDING
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 / cyclin-dependent protein kinase activity / G2 Phase / 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 / cyclin-dependent protein kinase activity / G2 Phase / 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 / Telomere Extension By Telomerase / G0 and Early G1 / 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 / male germ cell nucleus / positive regulation of DNA replication / meiotic cell cycle / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / Orc1 removal from chromatin / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / peptidyl-serine phosphorylation / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / chromosome, telomeric region / DNA replication / endosome / protein phosphorylation / chromatin remodeling / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / DNA-templated transcription / positive regulation of cell population proliferation / centrosome / 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
: / 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-7YG / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsBerg, S. / Bhat, R. / Anderson, M. / Bergh, M. / Brassington, C. / Hellberg, S. / Jerning, E. / Hogdin, K. / Lo-Alfredsson, Y. / Neelissen, J. ...Berg, S. / Bhat, R. / Anderson, M. / Bergh, M. / Brassington, C. / Hellberg, S. / Jerning, E. / Hogdin, K. / Lo-Alfredsson, Y. / Neelissen, J. / Nilsson, Y. / Ormo, M. / Soderman, P. / Stanway, J. / Tucker, J. / von Berg, S. / Weigelt, T. / Xue, Y.
CitationJournal: J. Med. Chem. / Year: 2012
Title: Discovery of novel potent and highly selective glycogen synthase kinase-3 beta (GSK3 beta ) inhibitors for Alzheimer's disease: design, synthesis, and characterization of pyrazines.
Authors: Berg, S. / Bergh, M. / Hellberg, S. / Hogdin, K. / Lo-Alfredsson, Y. / Soderman, P. / von Berg, S. / Weigelt, T. / Ormo, M. / Xue, Y. / Tucker, J. / Neelissen, J. / Jerning, E. / Nilsson, Y. / Bhat, R.
History
DepositionDec 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Feb 14, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYCLIN-DEPENDENT KINASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6284
Polymers34,0031
Non-polymers6263
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.430, 71.810, 72.040
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 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
Details: ACETYLATION AT N-TERMINAL METHIONINE / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF21 / References: UniProt: P24941, cyclin-dependent kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-7YG / 3-AMINO-6-(4-{[2-(DIMETHYLAMINO)ETHYL]SULFAMOYL}PHENYL)-N-PYRIDIN-3-YLPYRAZINE-2-CARBOXAMIDE


Mass: 441.507 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N7O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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 Å3/Da / Density % sol: 39.7 % / Description: NONE
Crystal growDetails: 8% PEG 3350, 0.1M HEPES PH 7.5, 0.05M AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2001
RadiationMonochromator: SI(311) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.63→29.88 Å / Num. obs: 26915 / % possible obs: 74.3 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 26.59 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.8
Reflection shellResolution: 1.63→1.71 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.2 / % possible all: 8.9

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE CDK2 MODEL

Resolution: 1.63→29.87 Å / Cor.coef. Fo:Fc: 0.9389 / Cor.coef. Fo:Fc free: 0.9276 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.13 / SU Rfree Blow DPI: 0.12 / SU Rfree Cruickshank DPI: 0.118
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 1333 4.97 %RANDOM
Rwork0.1836 ---
obs0.1854 26843 76.11 %-
Displacement parametersBiso mean: 34.34 Å2
Baniso -1Baniso -2Baniso -3
1-3.651 Å20 Å20 Å2
2---9.4468 Å20 Å2
3---5.7958 Å2
Refine analyzeLuzzati coordinate error obs: 0.214 Å
Refinement stepCycle: LAST / Resolution: 1.63→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2161 0 43 183 2387
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012384HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.033263HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d785SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes42HARMONIC2
X-RAY DIFFRACTIONt_gen_planes348HARMONIC5
X-RAY DIFFRACTIONt_it2384HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion18.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion303SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies14HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3016SEMIHARMONIC4
LS refinement shellResolution: 1.63→1.7 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2531 8 2.22 %
Rwork0.3083 353 -
all0.3071 361 -
obs--76.11 %
Refinement TLS params.Method: refined / Origin x: 2.8543 Å / Origin y: 30.8176 Å / Origin z: 22.7325 Å
111213212223313233
T-0.0614 Å2-0.0011 Å2-0.0002 Å2--0.0812 Å20.0156 Å2---0.0634 Å2
L1.1852 °20.3106 °2-0.1712 °2-0.3579 °2-0.074 °2--2.0669 °2
S0.0337 Å °0.0805 Å °0.045 Å °0.0074 Å °-0.0063 Å °0.0962 Å °0.0126 Å °-0.0284 Å °-0.0274 Å °
Refinement TLS groupSelection details: CHAIN A

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