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

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Basic information

Entry
Database: PDB / ID: 11gy
TitleCrystal structure of selective inhibitor 16 bound at the active site of CDK1
Components
  • (Cyclin-dependent ...) x 2
  • G2/mitotic-specific cyclin-B1
KeywordsSIGNALING PROTEIN / kinase / cancer / oncology / inhibitor / selectivity
Function / homology
Function and homology information


regulation of Schwann cell differentiation / cyclin A1-CDK1 complex / regulation of attachment of mitotic spindle microtubules to kinetochore / pronuclear fusion / mitotic cell cycle phase transition / response to DDT / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / regulation of chromosome condensation / Mitotic Prophase ...regulation of Schwann cell differentiation / cyclin A1-CDK1 complex / regulation of attachment of mitotic spindle microtubules to kinetochore / pronuclear fusion / mitotic cell cycle phase transition / response to DDT / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / regulation of chromosome condensation / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / histone kinase activity / Golgi disassembly / E2F-enabled inhibition of pre-replication complex formation / ventricular cardiac muscle cell development / microtubule cytoskeleton organization involved in mitosis / Depolymerization of the Nuclear Lamina / positive regulation of mRNA 3'-end processing / regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of attachment of spindle microtubules to kinetochore / MASTL Facilitates Mitotic Progression / Activation of NIMA Kinases NEK9, NEK6, NEK7 / patched binding / cyclin A2-CDK1 complex / Phosphorylation of Emi1 / mitotic nuclear membrane disassembly / Transcriptional regulation by RUNX2 / Nuclear Pore Complex (NPC) Disassembly / tissue regeneration / Phosphorylation of the APC/C / G2/M DNA replication checkpoint / outer kinetochore / protein localization to kinetochore / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Initiation of Nuclear Envelope (NE) Reformation / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / meiosis I / cellular response to fatty acid / cyclin-dependent protein serine/threonine kinase activator activity / oocyte maturation / [RNA-polymerase]-subunit kinase / chromosome condensation / digestive tract development / Condensation of Prometaphase Chromosomes / response to amine / positive regulation of ubiquitin-dependent protein catabolic process / centrosome cycle / cyclin-dependent protein serine/threonine kinase regulator activity / peptidyl-threonine phosphorylation / response to copper ion / mitotic metaphase chromosome alignment / SCF ubiquitin ligase complex / cyclin-dependent protein kinase activity / regulation of heterochromatin organization / MAPK3 (ERK1) activation / G1/S-Specific Transcription / mitotic G2 DNA damage checkpoint signaling / Regulation of APC/C activators between G1/S and early anaphase / microtubule organizing center / regulation of embryonic development / ubiquitin-like protein ligase binding / positive regulation of G2/M transition of mitotic cell cycle / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / response to cadmium ion / response to axon injury / protein deubiquitination / response to mechanical stimulus / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / positive regulation of cardiac muscle cell proliferation / cyclin-dependent protein kinase holoenzyme complex / Cyclin A/B1/B2 associated events during G2/M transition / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / ERK1 and ERK2 cascade / Nuclear events stimulated by ALK signaling in cancer / epithelial cell differentiation / RNA polymerase II CTD heptapeptide repeat kinase activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / positive regulation of mitotic cell cycle / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / negative regulation of protein ubiquitination / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / regulation of mitotic cell cycle / Hsp70 protein binding / APC/C:Cdc20 mediated degradation of Cyclin B / AURKA Activation by TPX2 / cyclin binding / positive regulation of DNA replication / Resolution of Sister Chromatid Cohesion / mitotic spindle organization / response to activity / Condensation of Prophase Chromosomes / spindle microtubule / cellular response to iron(III) ion / ubiquitin binding / G1/S transition of mitotic cell cycle
Similarity search - Function
: / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / : / Cyclin, C-terminal domain / : ...: / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / : / 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
: / : / Cyclin-dependent kinase 1 / G2/mitotic-specific cyclin-B1 / Cyclin-dependent kinases regulatory subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.0Jul 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclin-dependent kinase 1
B: G2/mitotic-specific cyclin-B1
C: Cyclin-dependent kinases regulatory subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,40915
Polymers77,6983
Non-polymers1,71112
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.699, 75.699, 254.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Cyclin-dependent ... , 2 types, 2 molecules AC

#1: Protein Cyclin-dependent kinase 1 / CDK1 / Cell division control protein 2 homolog / Cell division protein kinase 1 / p34 protein kinase


Mass: 36435.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK1, CDC2, CDC28A, CDKN1, P34CDC2 / Production host: Escherichia coli (E. coli)
References: UniProt: P06493, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#3: Protein Cyclin-dependent kinases regulatory subunit 2 / CKS-2


Mass: 9892.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CKS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P33552

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Protein , 1 types, 1 molecules B

#2: Protein G2/mitotic-specific cyclin-B1


Mass: 31369.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNB1, CCNB / Production host: Escherichia coli (E. coli) / References: UniProt: P14635

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Non-polymers , 7 types, 288 molecules

#4: 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.: 1 / Source method: obtained synthetically / Formula: C19H24N6O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A1DJL / (6S,9R,13S)-6,9-dimethyl-2,5,8,11-tetraoxatetradecan-13-amine / Jeffamine fragment


Mass: 249.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H27NO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#9: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.16M (NH4)2SO4, 24% PEG 4000, 0.02M HEPES pH 7.5, 14% 2-methyl-2,4-pentandiol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18071 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18071 Å / Relative weight: 1
ReflectionResolution: 2.4→35 Å / Num. obs: 28432 / % possible obs: 93.7 % / Redundancy: 4.8 % / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.05 / Rrim(I) all: 0.123 / Χ2: 1.052 / Net I/σ(I): 6.9 / Num. measured all: 137110
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.4-2.442.40.447310.5230.8290.2680.5220.64949.5
2.44-2.492.60.4549990.6140.8720.2790.5390.73367.7
2.49-2.532.80.40712120.7290.9180.2410.4780.6781.2
2.53-2.5930.39513410.6760.8980.2350.4650.67391.8
2.59-2.643.60.39614230.6480.8870.2240.4590.66596
2.64-2.74.10.36714780.7710.9330.1920.4170.70798.6
2.7-2.774.40.32214450.8250.9510.1630.3630.71898.6
2.77-2.854.30.29214810.8590.9610.1490.330.72398.5
2.85-2.934.90.26114900.9170.9780.1240.290.78899
2.93-3.0250.23314570.9430.9850.1080.2580.86598.6
3.02-3.135.20.20614920.9480.9870.0950.2290.999.2
3.13-3.264.90.18515000.9590.9890.0870.2050.99199.3
3.26-3.45.20.15414840.9760.9940.070.171.11299.1
3.4-3.585.70.13415130.9810.9950.0580.1471.18499.5
3.58-3.815.70.11115170.9880.9970.0480.1211.41999.2
3.81-4.160.114980.990.9980.0420.1081.47399.5
4.1-4.5160.08615410.9940.9980.0350.0931.51898.8
4.51-5.175.90.07915330.9940.9980.0330.0861.38398.8
5.17-6.560.07215860.9950.9990.030.0781.03999.4
6.5-355.80.05617110.9970.9990.0240.0611.04498.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→34.6 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.922 / SU B: 17.897 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.493 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23062 1373 4.8 %RANDOM
Rwork0.18589 ---
obs0.18807 26942 94.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.039 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å2-0 Å20 Å2
2---0.81 Å2-0 Å2
3---1.61 Å2
Refinement stepCycle: 1 / Resolution: 2.4→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5127 0 106 276 5509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125362
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165118
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.8487266
X-RAY DIFFRACTIONr_angle_other_deg0.4451.7711788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.691530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11110941
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0520.2812
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026075
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021189
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2594.3072540
X-RAY DIFFRACTIONr_mcbond_other2.2574.3072540
X-RAY DIFFRACTIONr_mcangle_it3.7087.7323169
X-RAY DIFFRACTIONr_mcangle_other3.7087.7323170
X-RAY DIFFRACTIONr_scbond_it2.494.6362822
X-RAY DIFFRACTIONr_scbond_other2.3884.5872797
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.878.3324055
X-RAY DIFFRACTIONr_long_range_B_refined6.6441.66194
X-RAY DIFFRACTIONr_long_range_B_other6.54941.076115
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 68 -
Rwork0.277 1160 -
obs--56.64 %
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)
11.8204-0.74980.59140.61280.12881.29710.13640.0457-0.0883-0.013-0.12090.06980.1641-0.0389-0.01550.29830.0187-0.00930.208-0.0270.0285-2.928-35.9121.837
20.4899-0.0712-0.00811.29410.84572.0448-0.0156-0.0708-0.0133-0.03780.0895-0.0584-0.17240.0937-0.07390.24270.01960.00790.2872-0.01350.0045-14.448-11.33322.367
33.8706-0.07660.37272.17730.72483.91930.2103-0.0066-0.49470.0197-0.05850.03440.5072-0.0418-0.15180.38830.0637-0.07090.1715-0.0060.13817.329-53.8120.181
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 401
2X-RAY DIFFRACTION2B162 - 504
3X-RAY DIFFRACTION3C1 - 76

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