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- PDB-4fkg: Crystal structure of the cdk2 in complex with aminopyrazole inhibitor -

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Basic information

Entry
Database: PDB / ID: 4fkg
TitleCrystal structure of the cdk2 in complex with aminopyrazole inhibitor
ComponentsCyclin-dependent kinase 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / ALPHA AND BETA PROTEIN (A+B) / TRANSFERASE / 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 / Activation of ATR in response to replication stress / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cajal body / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / Cyclin A/B1/B2 associated events during G2/M transition / 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 / regulation of mitotic cell cycle / cyclin binding / positive regulation of DNA replication / meiotic cell cycle / male germ cell nucleus / G1/S transition of mitotic cell cycle / peptidyl-serine phosphorylation / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / 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 / DNA replication / chromosome, telomeric region / 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-4CK / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsKang, Y.N. / Stuckey, J.A.
CitationJournal: To be Published
Title: Crystal structure of the cdk2 in complex with aminopyrazole inhibitor
Authors: Kang, Y.N. / Stuckey, J.A.
History
DepositionJun 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Other
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)34,2742
Polymers34,0031
Non-polymers2711
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.305, 71.634, 72.407
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
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Plasmid: PFB1 / Cell line (production host): HIGH-FIVE / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P24941, cyclin-dependent kinase
#2: Chemical ChemComp-4CK / 4-[(5-cyclopropyl-1H-pyrazol-3-yl)carbamoyl]benzoic acid


Mass: 271.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 15-20% PEG3350, 0.2M AMMONIUM ACETATE, 0.1M HEPES, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K, VAPOR DIFFUSION, SITTING DROP, pH 7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 / 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: 1.51→50 Å / Num. all: 44045 / Num. obs: 43429 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 15.4
Reflection shellResolution: 1.51→1.54 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.397 / % possible all: 78.6

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Processing

Software
NameVersionClassification
MD2data collection
PHASERphasing
BUSTER2.11.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R3I

2r3i


Resolution: 1.51→36.82 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2195 5.06 %RANDOM
Rwork0.179 ---
obs0.181 43362 98 %-
Displacement parametersBiso mean: 29.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.2222 Å20 Å20 Å2
2---1.4732 Å20 Å2
3---2.6954 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.51→36.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2276 0 20 214 2510
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012527HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.053470HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1201SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes392HARMONIC5
X-RAY DIFFRACTIONt_it2527HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion3.47
X-RAY DIFFRACTIONt_chiral_improper_torsion329SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3134SEMIHARMONIC4
LS refinement shellResolution: 1.51→1.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2333 129 5.23 %
Rwork0.2205 2337 -
all0.2211 2466 -
obs--98.05 %
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)
13.30891.8243-2.19334.5489-1.05720-0.07270.1559-0.23060.0560.03710.01380.164-0.14650.0356-0.03070.0086-0.06460.0112-0.07390.0223-5.7943-9.0162-34.2885
22.916-0.4279-0.5850.7784-0.32731.9843-0.1220.1736-0.1058-0.0132-0.00920.3392-0.0374-0.46890.1311-0.09510.01-0.0191-0.00940.01750.0192-8.8122-0.0527-29.2592
30.67490.18110.76350.8543-0.44042.1549-0.01440.14510.0054-0.0626-0.02850.06380.15030.19880.0429-0.03990.02510.016-0.03430.0328-0.05036.2576-2.6696-19.1788
41.58470.60471.979400.19432.50690.0156-0.0126-0.014-0.1372-0.03390.062-0.0405-0.33470.0183-0.02490.0136-0.01510.01180.0513-0.002-2.5682-1.468-20.0421
51.35010.2653-0.12860.6568-0.61120.86290.1051-0.0139-0.0624-0.0576-0.05970.0370.1241-0.052-0.0454-0.0045-0.0145-0.0015-0.03610.0084-0.0408-0.1476-12.7888-3.688
61.34910.550.43970.6819-0.15550.46670.07020.0074-0.00690.0973-0.0505-0.0597-0.02480.1543-0.0197-0.0037-0.00110.00940.00350.0073-0.037712.807-2.5559-4.9582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - 16}
2X-RAY DIFFRACTION2{A|17 - 77}
3X-RAY DIFFRACTION3{A|78 - 137}
4X-RAY DIFFRACTION4{A|138 - 153}
5X-RAY DIFFRACTION5{A|157 - 241}
6X-RAY DIFFRACTION6{A|242 - 298}

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