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- PDB-9gp3: Crystal structure of CDK2-cyclin E1 bound by compound 11 (AZD8421) -

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Basic information

Entry
Database: PDB / ID: 9gp3
TitleCrystal structure of CDK2-cyclin E1 bound by compound 11 (AZD8421)
Components
  • Cyclin-dependent kinase 2
  • G1/S-specific cyclin-E1
KeywordsTRANSFERASE / kinase / CDK2 / inhibitor / AZD8421
Function / homology
Function and homology information


positive regulation of mesenchymal stem cell proliferation / RHOBTB3 ATPase cycle / cyclin-dependent protein serine/threonine kinase regulator activity / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / G2 Phase / Y chromosome / cyclin-dependent protein kinase activity ...positive regulation of mesenchymal stem cell proliferation / RHOBTB3 ATPase cycle / cyclin-dependent protein serine/threonine kinase regulator activity / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / G2 Phase / Y chromosome / cyclin-dependent protein kinase activity / regulation of heterochromatin organization / 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 / G1/S-Specific Transcription / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Association of TriC/CCT with target proteins during biosynthesis / Regulation of APC/C activators between G1/S and early anaphase / telomere maintenance in response to DNA damage / microtubule organizing center / G0 and Early G1 / centrosome duplication / 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 / positive regulation of G1/S transition of mitotic cell cycle / 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-dependent protein kinase holoenzyme complex / Cyclin A:Cdk2-associated events at S phase entry / Cyclin A/B1/B2 associated events during G2/M transition / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / cellular response to nitric oxide / negative regulation of protein localization to chromatin / post-translational protein modification / regulation of mitotic cell cycle / cyclin binding / positive regulation of DNA replication / peptidyl-serine phosphorylation / G1/S transition of mitotic cell cycle / meiotic cell cycle / DNA Damage/Telomere Stress Induced Senescence / cellular senescence / G2/M transition of mitotic cell cycle / Meiotic recombination / CDK-mediated phosphorylation and removal of Cdc6 / Transcriptional regulation of granulopoiesis / SCF(Skp2)-mediated degradation of p27/p21 / kinase activity / Orc1 removal from chromatin / Cyclin D associated events in G1 / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / transcription regulator complex / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Regulation of TP53 Activity through Phosphorylation / Ras protein signal transduction / ciliary basal body / protein phosphorylation / chromosome, telomeric region / DNA replication / endosome / chromatin remodeling / protein domain specific binding / protein serine kinase activity / cell division / DNA repair / protein serine/threonine kinase activity / positive regulation of cell population proliferation / centrosome / protein kinase binding / magnesium ion binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma ...Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / 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
Similarity search - Domain/homology
: / G1/S-specific cyclin-E1 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsCollie, G.W. / Pflug, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery of AZD8421: A Potent CDK2 Inhibitor with Selectivity Against Other CDK Family Members and the Human Kinome.
Authors: Ghosh, A. / Ahmed, A. / Amoiradaki, K. / Balazs, A.Y.S. / Barlaam, B. / Bodnarchuk, M.S. / Collie, G.W. / Dale, I.L. / Denz, C.R. / Drew, L. / Edmondson, S.D. / Fan, J. / Fawell, S. / ...Authors: Ghosh, A. / Ahmed, A. / Amoiradaki, K. / Balazs, A.Y.S. / Barlaam, B. / Bodnarchuk, M.S. / Collie, G.W. / Dale, I.L. / Denz, C.R. / Drew, L. / Edmondson, S.D. / Fan, J. / Fawell, S. / Goldberg, F.W. / Gopalsamy, A. / Grondine, M. / Guo, G. / Hande, S.M. / Hatoum-Mokdad, H. / Hird, A.W. / Howells, R. / Hao-Ru Hsu, J. / Hudson, J. / Jackson, A. / Lamb, M.L. / Lamont, G.M. / Lamont, S. / Lichtor, P.A. / McWilliams, L. / Milne, D. / Mlynarski, S.N. / Narasimhan, P. / Peters, M.F. / Pflug, A. / Pollard, H.K. / Qin, M. / Reimer, C. / Robbins, K.J. / Robinson, J. / Sha, L. / She, H. / Sheppeck 2nd, J.E. / Singh, B. / Song, K. / Su, Q. / Telmesani, R. / Throner, S. / Vasalou, C. / Wang, L. / Wang, Y. / Wilson, D.M. / Winlow, P. / Yang, W. / Yao, T. / Zhang, Y. / Zhang, Z. / Zindel, D. / Johannes, J.W.
History
DepositionSep 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 24, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclin-dependent kinase 2
B: G1/S-specific cyclin-E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4713
Polymers67,0302
Non-polymers4411
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-6 kcal/mol
Surface area24420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.629, 100.629, 150.06
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cyclin-dependent kinase 2 / 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) / Gene: CDK2, CDKN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, cyclin-dependent kinase
#2: Protein G1/S-specific cyclin-E1


Mass: 33053.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNE1, CCNE / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24864
#3: Chemical ChemComp-A1IOP / (3~{S})-~{N}-ethyl-3-[[9-ethyl-2-[[(2~{R},3~{S})-2-oxidanylpentan-3-yl]amino]purin-6-yl]amino]pyrrolidine-1-sulfonamide


Mass: 440.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H32N8O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.83 Å3/Da / Density % sol: 56.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 8-15% PEG3350 / 0.2M Na3Cit pH8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.45→83.58 Å / Num. obs: 22205 / % possible obs: 95.1 % / Redundancy: 13.2 % / CC1/2: 1 / Net I/σ(I): 17.9
Reflection shellResolution: 2.45→2.65 Å / Num. unique obs: 1110 / CC1/2: 0.677

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→83.58 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.681 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.679 / SU Rfree Blow DPI: 0.326 / SU Rfree Cruickshank DPI: 0.331
RfactorNum. reflection% reflectionSelection details
Rfree0.2726 1026 -RANDOM
Rwork0.2334 ---
obs0.2352 22204 76.7 %-
Displacement parametersBiso mean: 76 Å2
Baniso -1Baniso -2Baniso -3
1--0.0789 Å20 Å20 Å2
2---0.0789 Å20 Å2
3---0.1577 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.45→83.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4533 0 30 27 4590
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074678HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.96355HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1612SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes765HARMONIC5
X-RAY DIFFRACTIONt_it4678HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion602SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3683SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion18.67
LS refinement shellResolution: 2.45→2.56 Å
RfactorNum. reflection% reflection
Rfree0.4405 20 -
Rwork0.3349 --
obs0.34 445 12.46 %

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