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- PDB-11gv: Crystal structure of selective inhibitor 16 bound at the active s... -

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Basic information

Entry
Database: PDB / ID: 11gv
TitleCrystal structure of selective inhibitor 16 bound at the active site of CDK2
Components
  • Cyclin-A2
  • Cyclin-dependent kinase 2
KeywordsSIGNALING PROTEIN / kinase / cancer / oncology / inhibitor / selectivity
Function / homology
Function and homology information


cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / G2/M DNA replication checkpoint / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / response to glucagon / male pronucleus / female pronucleus / cellular response to cocaine / cyclin-dependent protein serine/threonine kinase regulator activity ...cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / G2/M DNA replication checkpoint / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / response to glucagon / male pronucleus / female pronucleus / cellular response to cocaine / 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 / 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 / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / telomere maintenance in response to DNA damage / Regulation of APC/C activators between G1/S and early anaphase / animal organ regeneration / microtubule organizing center / regulation of DNA replication / G0 and Early G1 / cochlea development / Activation of the pre-replicative complex / cellular response to platelet-derived growth factor stimulus / Telomere Extension By Telomerase / cyclin-dependent protein kinase holoenzyme 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 / Cyclin E associated events during G1/S transition / Activation of ATR in response to replication stress / centrosome duplication / Cyclin A:Cdk2-associated events at S phase entry / Cyclin A/B1/B2 associated events during G2/M transition / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / cellular response to nitric oxide / post-translational protein modification / positive regulation of fibroblast proliferation / cyclin binding / positive regulation of DNA replication / negative regulation of protein localization to chromatin / regulation of mitotic cell cycle / cellular response to estradiol stimulus / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / meiotic cell cycle / peptidyl-serine phosphorylation / cellular senescence / 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 / Cyclin D associated events in G1 / Regulation of TP53 Degradation / nuclear envelope / transcription regulator complex / Factors involved in megakaryocyte development and platelet production / ciliary basal body / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / Ras protein signal transduction / DNA replication / protein phosphorylation / chromosome, telomeric region / endosome / Ub-specific processing proteases / chromatin remodeling / cell division / protein domain specific binding / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / positive regulation of cell population proliferation / protein kinase binding / magnesium ion binding / signal transduction / nucleoplasm
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, N-terminal ...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, 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
: / ISOPROPYL ALCOHOL / Cyclin-A2 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsMurray, J.M. / Oh, A. / Kiefer, J.R. / Verma, V.A. / Grandner, J.M. / Parr, B.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2026
Title: Utilizing Molecular Dynamics and Mechanistic Pharmacokinetic Studies in the Design of Selective CDK2 Inhibitors.
Authors: Verma, V.A. / Grandner, J.M. / Parr, B.T. / Zeng, M. / Ashley, M. / Wang, Y. / Beroza, P. / Carione, P. / Johnson, K.M. / Oh, A.J. / Murray, J.M. / Kiefer, J.R. / Moffat, J.G. / Prangley, M. ...Authors: Verma, V.A. / Grandner, J.M. / Parr, B.T. / Zeng, M. / Ashley, M. / Wang, Y. / Beroza, P. / Carione, P. / Johnson, K.M. / Oh, A.J. / Murray, J.M. / Kiefer, J.R. / Moffat, J.G. / Prangley, M. / Merrick, K. / Vartanian, S. / Hafner, M. / Orr, C.J. / Segal, E. / Levy, E.S. / Wang, J. / Xu, Z. / Wang, S. / Liu, G. / Niu, Y. / Li, X. / Zhang, Q. / Ma, Z. / Sun, M. / Wu, Z. / Zhao, W. / Li, Y. / Zhang, L. / Magnuson, S.R. / Samy, K.E.
History
DepositionFeb 23, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclin-dependent kinase 2
B: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,39834
Polymers63,9412
Non-polymers2,45732
Water11,998666
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-22 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.930, 112.230, 159.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

21A-675-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Cyclin-dependent kinase 2 / Cell division protein kinase 2 / p33 protein kinase


Mass: 34056.469 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 Cyclin-A2 / Cyclin-A / Cyclin A


Mass: 29884.605 Da / Num. of mol.: 1 / Fragment: residues 174-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNA2, CCN1, CCNA / Production host: Escherichia coli (E. coli) / References: UniProt: P20248

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Non-polymers , 7 types, 698 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-A1DEQ / (1R,3S)-3-{3-[(1-methyl-6-oxo-1,6-dihydropyrimidin-2-yl)amino]-1H-pyrazol-5-yl}cyclopentyl bicyclo[1.1.1]pentan-1-ylcarbamate


Mass: 384.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24N6O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 15% ethylene glycol, 10% 2-propanol, 0.2M MgCl2, 10% PEG 4000, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.59→29.52 Å / Num. obs: 85637 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.018 / Rrim(I) all: 0.068 / Χ2: 0.97 / Net I/σ(I): 20.9 / Num. measured all: 1166101
Reflection shellResolution: 1.59→1.62 Å / % possible obs: 97.8 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.746 / Num. measured all: 54598 / Num. unique obs: 4138 / CC1/2: 0.916 / Rpim(I) all: 0.208 / Rrim(I) all: 0.775 / Χ2: 0.87 / Net I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→29.52 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1942 4304 5.03 %
Rwork0.1694 --
obs0.1706 85582 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4377 0 155 666 5198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034726
X-RAY DIFFRACTIONf_angle_d0.8136412
X-RAY DIFFRACTIONf_dihedral_angle_d14.1241725
X-RAY DIFFRACTIONf_chiral_restr0.045721
X-RAY DIFFRACTIONf_plane_restr0.005804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.610.31991290.24732608X-RAY DIFFRACTION97
1.61-1.630.25831410.23642688X-RAY DIFFRACTION100
1.63-1.650.26371570.23172679X-RAY DIFFRACTION100
1.65-1.670.23281490.21512675X-RAY DIFFRACTION100
1.67-1.690.26841430.22092682X-RAY DIFFRACTION100
1.69-1.710.23261630.21052656X-RAY DIFFRACTION100
1.71-1.740.22131580.1982677X-RAY DIFFRACTION100
1.74-1.760.21131610.19162641X-RAY DIFFRACTION100
1.76-1.790.21071270.18692747X-RAY DIFFRACTION100
1.79-1.820.22981380.18642684X-RAY DIFFRACTION100
1.82-1.850.24111530.18512679X-RAY DIFFRACTION100
1.85-1.890.18711580.17912667X-RAY DIFFRACTION100
1.89-1.920.22791380.18382699X-RAY DIFFRACTION100
1.92-1.960.24111390.18542717X-RAY DIFFRACTION100
1.96-20.20631420.18562688X-RAY DIFFRACTION100
2-2.050.20921070.18012707X-RAY DIFFRACTION100
2.05-2.10.20161250.16612737X-RAY DIFFRACTION100
2.1-2.160.20131650.16862685X-RAY DIFFRACTION100
2.16-2.220.18971360.16662731X-RAY DIFFRACTION100
2.22-2.290.20541700.16782687X-RAY DIFFRACTION100
2.29-2.370.19351600.16232690X-RAY DIFFRACTION100
2.37-2.470.20651360.16592715X-RAY DIFFRACTION100
2.47-2.580.21221300.17122712X-RAY DIFFRACTION100
2.58-2.720.20091570.17352704X-RAY DIFFRACTION100
2.72-2.890.18241300.16722763X-RAY DIFFRACTION100
2.89-3.110.18961160.16892748X-RAY DIFFRACTION100
3.11-3.420.16561260.16062763X-RAY DIFFRACTION100
3.42-3.920.1691520.14962774X-RAY DIFFRACTION100
3.92-4.930.15991550.14392763X-RAY DIFFRACTION100
4.93-29.520.1921430.17472912X-RAY DIFFRACTION100
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)
10.1843-0.15110.10140.1814-0.02450.2646-0.0286-0.062-0.1009-0.01760.1052-0.05150.23640.03980.00110.3407-0.05650.10550.2155-0.02280.1814-14.9894-31.461230.1607
21.63450.82440.10860.5011-0.36491.04350.02680.0831-0.18220.2088-0.0559-0.12550.08040.1222-0.00360.2425-0.04860.07440.184-0.0190.1498-5.2577-23.174324.5161
34.8987-0.64011.71811.673-0.77333.46330.2906-0.0861-0.43750.09890.0050.34820.4149-0.12830.28290.2568-0.12070.17520.11770.00510.2304-18.5065-25.16723.715
40.61470.08870.12560.5867-0.15070.73390.1253-0.04340.00920.60110.00070.41310.0468-0.14240.07330.2025-0.03870.19410.17430.02630.2652-18.4123-13.546217.4392
50.51880.05740.1511.1316-0.30361.85590.08760.0898-0.0224-0.0523-0.02190.16450.11990.06880.00150.12710.00230.00970.14420.00480.1755-12.1113-16.31370.8306
60.0354-0.04230.0310.0895-0.11750.36460.14670.14790.38570.12440.00160.5770.0319-0.28930.01080.14410.00570.03670.26170.06480.4414-27.665-7.1612.2271
70.46430.19720.51420.4829-0.06370.72360.0502-0.0190.32520.18010.06790.4042-0.1836-0.1960.00220.18080.00740.09180.19670.02990.3228-19.3232-3.577.7892
80.97940.16630.09240.6950.39620.23450.1508-0.17530.2053-0.0834-0.00390.2005-0.0034-0.1940.00140.1879-0.05070.05370.2081-0.00520.2099-1.4393-0.489319.4387
91.3387-0.08830.09771.1495-0.371.0966-0.033-0.12110.10220.0989-0.0105-0.1636-0.00290.1044-0.00470.163-0.01470.0510.157-0.01120.124417.4456-16.583426.7358
101.16280.3160.04550.56910.25190.90460.018-0.0535-0.2033-0.01850.01790.00250.21510.11440.00210.2226-0.00570.06050.1776-0.00320.103212.1599-25.665723.9157
111.7521-0.0889-0.24372.2530.08451.48170.06950.03710.2852-0.2125-0.0464-0.2621-0.15570.05240.00010.1514-0.03640.08650.1195-0.0060.204418.69832.142116.4636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 100 )
4X-RAY DIFFRACTION4chain 'A' and (resid 101 through 140 )
5X-RAY DIFFRACTION5chain 'A' and (resid 141 through 247 )
6X-RAY DIFFRACTION6chain 'A' and (resid 248 through 266 )
7X-RAY DIFFRACTION7chain 'A' and (resid 267 through 290 )
8X-RAY DIFFRACTION8chain 'B' and (resid 174 through 192 )
9X-RAY DIFFRACTION9chain 'B' and (resid 193 through 268 )
10X-RAY DIFFRACTION10chain 'B' and (resid 269 through 310 )
11X-RAY DIFFRACTION11chain 'B' and (resid 311 through 432 )

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