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- PDB-3eoc: Cdk2/CyclinA complexed with a imidazo triazin-2-amine -

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Basic information

Entry
Database: PDB / ID: 3eoc
TitleCdk2/CyclinA complexed with a imidazo triazin-2-amine
Components
  • Cell division protein kinase 2
  • Cyclin-A2
KeywordsTRANSFERASE/CELL CYCLE / cdk / cyclin / ATP-binding / Cell cycle / Cell division / Kinase / Mitosis / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Transferase / Nucleus / TRANSFERASE-CELL CYCLE COMPLEX
Function / homology
Function and homology information


Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine ...Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity / positive regulation of DNA biosynthetic process / cellular response to insulin-like growth factor stimulus / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cochlea development / 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 / regulation of DNA replication / cellular response to platelet-derived growth factor stimulus / 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 / cellular response to nitric oxide / 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 / animal organ regeneration / 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 / Cajal body / Cyclin A/B1/B2 associated events during G2/M transition / cyclin-dependent protein kinase holoenzyme complex / 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 / regulation of mitotic cell cycle / post-translational protein modification / cyclin binding / positive regulation of DNA replication / male germ cell nucleus / meiotic cell cycle / cellular response to estradiol stimulus / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / 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 / Transcriptional regulation of granulopoiesis / Orc1 removal from chromatin / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / cellular senescence / positive regulation of fibroblast proliferation / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / cellular response to hypoxia / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / DNA replication / chromosome, telomeric region / Ub-specific processing proteases / endosome / chromatin remodeling / protein phosphorylation / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / DNA-templated transcription / positive regulation of cell population proliferation / protein kinase binding
Similarity search - Function
Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin-like ...Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / 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
Chem-T2A / Cyclin-A2 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsCheung, M. / Kuntz, K. / Pobanz, M. / Salovich, J. / Wilson, B. / Andrews, W. / Shewchuk, L. / Epperly, A. / Hassler, D. / Leesnitzer, M. ...Cheung, M. / Kuntz, K. / Pobanz, M. / Salovich, J. / Wilson, B. / Andrews, W. / Shewchuk, L. / Epperly, A. / Hassler, D. / Leesnitzer, M. / Smith, J. / Smith, G. / Lansing, T. / Mook, R.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Imidazo[5,1-f][1,2,4]triazin-2-amines as novel inhibitors of polo-like kinase 1.
Authors: Cheung, M. / Kuntz, K.W. / Pobanz, M. / Salovich, J.M. / Wilson, B.J. / Andrews, C.W. / Shewchuk, L.M. / Epperly, A.H. / Hassler, D.F. / Leesnitzer, M.A. / Smith, J.L. / Smith, G.K. / Lansing, T.J. / Mook, R.A.
History
DepositionSep 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 6, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Cell division protein kinase 2
B: Cyclin-A2
C: Cell division protein kinase 2
D: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4716
Polymers127,6884
Non-polymers7832
Water00
1
A: Cell division protein kinase 2
B: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2353
Polymers63,8442
Non-polymers3911
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-11.9 kcal/mol
Surface area23590 Å2
MethodPISA
2
C: Cell division protein kinase 2
D: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2353
Polymers63,8442
Non-polymers3911
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-10.8 kcal/mol
Surface area23240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.977, 182.977, 213.687
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
12A
22C
13A
23C
14A
24C

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEU4BB180 - 4308 - 258
21GLUGLULEULEU4DD180 - 4308 - 258
12METMETPHEPHE4AA1 - 801 - 80
22METMETPHEPHE4CC1 - 801 - 80
13LEULEUHISHIS4AA83 - 29583 - 295
23LEULEUHISHIS4CC83 - 29583 - 295
14METMETMETMET1AA11
24METMETMETMET1CC11

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Cell division protein 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) / Gene: CDK2 / Plasmid: pFastbac / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24941, cyclin-dependent kinase
#2: Protein Cyclin-A2 / Cyclin-A


Mass: 29867.512 Da / Num. of mol.: 2 / Fragment: Proteolytic fragment: Residues 173-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNA2, CCN1, CCNA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20248
#3: Chemical ChemComp-T2A / 5-methyl-7-phenyl-N-(3,4,5-trimethoxyphenyl)imidazo[5,1-f][1,2,4]triazin-2-amine


Mass: 391.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H21N5O3

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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: 4.04 Å3/Da / Density % sol: 69.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 1.5 M Sodium acetate, 100 mM Sodium cacodylate pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 22, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 33305 / Num. obs: 33305 / % possible obs: 98.92 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.9
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2443 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
DENZOdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FVV

1fvv


Resolution: 3.2→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.926 / SU B: 47.092 / SU ML: 0.34 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23836 1737 5 %RANDOM
Rwork0.21462 ---
all0.21585 33305 --
obs0.21585 33305 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 93.243 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å21.16 Å20 Å2
2--2.32 Å20 Å2
3----3.48 Å2
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8714 0 58 0 8772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228994
X-RAY DIFFRACTIONr_angle_refined_deg1.0361.98712224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.74251096
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28224.044361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.124151552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9231538
X-RAY DIFFRACTIONr_chiral_restr0.0690.21400
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026752
X-RAY DIFFRACTIONr_nbd_refined0.1840.24061
X-RAY DIFFRACTIONr_nbtor_refined0.3010.26165
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2201
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.26
X-RAY DIFFRACTIONr_mcbond_it0.1911.55656
X-RAY DIFFRACTIONr_mcangle_it0.35428943
X-RAY DIFFRACTIONr_scbond_it0.40433789
X-RAY DIFFRACTIONr_scangle_it0.6964.53281
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
4A29tight positional0.010.05
1B1995medium positional0.260.5
2A579medium positional0.220.5
3A1677medium positional0.230.5
4A29tight thermal2.990.5
1B1995medium thermal0.142
2A579medium thermal0.142
3A1677medium thermal0.132
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 109 -
Rwork0.348 2443 -
obs-2443 99.26 %
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)
13.165-0.313-2.45887.41892.92255.2076-0.09770.5109-0.2694-0.2996-0.33951.04840.0435-0.72150.4372-0.06850.10990.0876-0.216-0.0307-0.2628-3.961584.116534.1713
20.95670.3642-0.03626.00873.83788.3777-0.42370.0538-0.2369-0.2185-0.36481.0858-0.1267-0.94550.7886-0.0512-0.18940.4065-0.0857-0.20.1742-15.213963.077151.5066
31.97-0.3414-0.93145.0127-0.74034.0562-0.06770.13570.1049-0.5685-0.0533-0.5574-0.07860.18690.121-0.1327-0.00490.168-0.23130.0022-0.361417.825391.271719.623
44.5560.5915-1.19093.008-0.39555.9766-0.0357-0.6311-0.8185-0.1983-0.1947-0.4210.3953-0.23190.2304-0.2408-0.10610.3546-0.16710.17340.2048-11.551450.961675.8997
54.8373-0.6352-0.5222.72580.96732.8969-0.39320.2447-0.39490.08780.02410.08980.43030.04440.3691-0.0340.06190.3144-0.324-0.0482-0.30512.032556.525929.4574
62.5886-0.42861.09182.52520.67524.7218-0.2375-0.2779-0.34820.0971-0.0872-0.3690.01540.04190.3247-0.3067-0.06070.2128-0.28550.0314-0.14732.310683.715769.4855
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 82
2X-RAY DIFFRACTION2C1 - 82
3X-RAY DIFFRACTION3A83 - 298
4X-RAY DIFFRACTION4C83 - 296
5X-RAY DIFFRACTION5B176 - 432
6X-RAY DIFFRACTION6D176 - 432

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