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- PDB-8i0m: Structure of CDK6 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 8i0m
TitleStructure of CDK6 in complex with inhibitor
ComponentsCyclin-dependent kinase 6
KeywordsCELL CYCLE/INHIBITOR / CDK6 / inhibitor / complex / CELL CYCLE / CELL CYCLE-INHIBITOR complex
Function / homology
Function and homology information


cyclin D2-CDK6 complex / cell dedifferentiation / Drug-mediated inhibition of CDK4/CDK6 activity / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / FBXO family protein binding / lateral ventricle development / negative regulation of myeloid cell differentiation / type B pancreatic cell development / negative regulation of monocyte differentiation ...cyclin D2-CDK6 complex / cell dedifferentiation / Drug-mediated inhibition of CDK4/CDK6 activity / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / FBXO family protein binding / lateral ventricle development / negative regulation of myeloid cell differentiation / type B pancreatic cell development / negative regulation of monocyte differentiation / astrocyte development / dentate gyrus development / gliogenesis / regulation of cell motility / Regulation of RUNX1 Expression and Activity / regulation of hematopoietic stem cell differentiation / positive regulation of cell-matrix adhesion / generation of neurons / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of cellular senescence / negative regulation of cell differentiation / negative regulation of cell cycle / hematopoietic stem cell differentiation / negative regulation of osteoblast differentiation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / Notch signaling pathway / ruffle / regulation of G2/M transition of mitotic cell cycle / cyclin binding / : / response to virus / regulation of erythrocyte differentiation / Oncogene Induced Senescence / G1/S transition of mitotic cell cycle / Cyclin D associated events in G1 / negative regulation of epithelial cell proliferation / positive regulation of fibroblast proliferation / T cell differentiation in thymus / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / Oxidative Stress Induced Senescence / regulation of cell cycle / negative regulation of cell population proliferation / cell division / protein phosphorylation / protein serine kinase activity / centrosome / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Cyclin-dependent kinase 6 / 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
Chem-NJ6 / Cyclin-dependent kinase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7772 Å
AuthorsJiang, C. / Ye, Y. / Huang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of CDK6 in complex with inhibitor
Authors: Jiang, C. / Ye, Y. / Huang, Y.
History
DepositionJan 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: 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 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5612
Polymers34,1901
Non-polymers3701
Water00
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)100.870, 100.870, 59.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Cyclin-dependent kinase 6 / Cell division protein kinase 6 / Serine/threonine-protein kinase PLSTIRE


Mass: 34190.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK6, CDKN6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q00534, cyclin-dependent kinase
#2: Chemical ChemComp-NJ6 / 2-[(4-azanylcyclohexyl)amino]-7-cyclopentyl-~{N},~{N}-dimethyl-pyrrolo[2,3-d]pyrimidine-6-carboxamide


Mass: 370.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30N6O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.2 M BIS-TRIS pH 7.0, 20% PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.772→27.45 Å / Num. obs: 7680 / % possible obs: 99.73 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1606 / Rpim(I) all: 0.04492 / Rrim(I) all: 0.1668 / Net I/σ(I): 15.71
Reflection shellResolution: 2.772→2.871 Å / Rmerge(I) obs: 2.314 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 739 / CC1/2: 0.565 / Rpim(I) all: 0.6895 / Rrim(I) all: 2.417 / % possible all: 98.53

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Processing

Software
NameVersionClassification
REFMAC7.1.010refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7772→27.45 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / SU B: 19.688 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2816 382 5 %RANDOM
Rwork0.203 ---
obs0.20665 7303 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.013 Å2
Baniso -1Baniso -2Baniso -3
1-2.47 Å20 Å20 Å2
2--2.47 Å20 Å2
3----4.94 Å2
Refinement stepCycle: 1 / Resolution: 2.7772→27.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 27 0 2080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132129
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172057
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.6442889
X-RAY DIFFRACTIONr_angle_other_deg1.2221.5794726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3365256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46221.091110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.04415352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1671516
X-RAY DIFFRACTIONr_chiral_restr0.0520.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022350
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02488
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_it6.0947.8091036
X-RAY DIFFRACTIONr_mcbond_other6.0937.8071035
X-RAY DIFFRACTIONr_mcangle_it8.7811.7241288
X-RAY DIFFRACTIONr_mcangle_other8.77711.7261289
X-RAY DIFFRACTIONr_scbond_it6.918.3441093
X-RAY DIFFRACTIONr_scbond_other6.9078.3421094
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.39112.2661602
LS refinement shellResolution: 2.7772→2.844 Å
RfactorNum. reflection% reflection
Rfree0.423 29 -
Rwork0.387 530 -
obs--98.07 %

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