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- PDB-3nup: CDK6 (monomeric) in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 3nup
TitleCDK6 (monomeric) in complex with inhibitor
ComponentsCell division protein kinase 6
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / Protein Kinase / ATP binding / phosphorylation / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


cyclin D2-CDK6 complex / cell dedifferentiation / 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 / Drug-mediated inhibition of CDK4/CDK6 activity / 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 / 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 / Drug-mediated inhibition of CDK4/CDK6 activity / 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 / regulation of cell motility / gliogenesis / Regulation of RUNX1 Expression and Activity / 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 cycle / hemopoiesis / negative regulation of cell differentiation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / negative regulation of osteoblast differentiation / cyclin-dependent protein kinase holoenzyme complex / ruffle / cyclin binding / regulation of erythrocyte differentiation / G1/S transition of mitotic cell cycle / Oncogene Induced Senescence / negative regulation of epithelial cell proliferation / G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / response to virus / Cyclin D associated events in G1 / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / regulation of cell cycle / negative regulation of cell population proliferation / protein serine kinase activity / cell division / centrosome / DNA damage response / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cyclin-dependent kinase 6 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Cyclin-dependent kinase 6 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-3NU / Cyclin-dependent kinase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChopra, R.
CitationJournal: J.Med.Chem. / Year: 2010
Title: 4-(Pyrazol-4-yl)-pyrimidines as selective inhibitors of cyclin-dependent kinase 4/6.
Authors: Cho, Y.S. / Borland, M. / Brain, C. / Chen, C.H. / Cheng, H. / Chopra, R. / Chung, K. / Groarke, J. / He, G. / Hou, Y. / Kim, S. / Kovats, S. / Lu, Y. / O'Reilly, M. / Shen, J. / Smith, T. / ...Authors: Cho, Y.S. / Borland, M. / Brain, C. / Chen, C.H. / Cheng, H. / Chopra, R. / Chung, K. / Groarke, J. / He, G. / Hou, Y. / Kim, S. / Kovats, S. / Lu, Y. / O'Reilly, M. / Shen, J. / Smith, T. / Trakshel, G. / Vogtle, M. / Xu, M. / Xu, M. / Sung, M.J.
History
DepositionJul 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3202
Polymers35,0191
Non-polymers3001
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.778, 101.778, 59.296
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

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


Mass: 35019.215 Da / Num. of mol.: 1 / Fragment: UNP residues 1-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q00534, cyclin-dependent kinase
#2: Chemical ChemComp-3NU / 4-[3-(1-methylethyl)-1H-pyrazol-4-yl]-N-(1-methylpiperidin-4-yl)pyrimidin-2-amine / 4-(3-isopropyl-1H-pyrazol-4-yl)-N-(1-methylpiperidin-4-yl)pyrimidin-2-amine


Mass: 300.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6
Details: 0.1M MES pH 6.0, 12% PEG3350, 0.1M NH4NO3, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Oct 10, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→19.96 Å / Num. obs: 10549 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.05 % / Rmerge(I) obs: 0.07 / Χ2: 1 / Net I/σ(I): 13.3 / Scaling rejects: 563
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.5-2.596.780.5382.5710710471.1199.1
2.59-2.696.850.4573711510361.0999.4
2.69-2.816.920.3783.5732910551.0799.6
2.81-2.967.040.2874.7731410371.0499.5
2.96-3.157.150.2026.5752610490.9999.8
3.15-3.397.220.1528.9771910650.9999.9
3.39-3.737.160.10312.7766910610.9699.8
3.73-4.267.150.06419.6757410520.8999.8
4.26-5.357.20.04727.3782710720.8699.9
5.35-19.967.020.03342.1775810750.9898.3

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Processing

Software
NameVersionClassificationNB
d*TREK9.6Ldata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
d*TREKdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CDK6

Resolution: 2.6→19.96 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 469 5 %RANDOM
Rwork0.2384 ---
all-9383 --
obs-9383 99.5 %-
Displacement parametersBiso max: 99.77 Å2 / Biso mean: 64.7972 Å2 / Biso min: 36.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2---0.35 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 22 24 2067
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5431.5
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_mcangle_it2.6572
X-RAY DIFFRACTIONc_scangle_it3.3992.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5ldz891.par

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