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- PDB-6gu7: CDK1/Cks2 in complex with AZD5438 -

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Basic information

Entry
Database: PDB / ID: 6gu7
TitleCDK1/Cks2 in complex with AZD5438
Components
  • Cyclin-dependent kinase 1
  • Cyclin-dependent kinases regulatory subunit 2
KeywordsCELL CYCLE / CDK1 / CKS2 / INHIBITOR
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 / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / histone kinase activity ...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 / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / histone kinase activity / Golgi disassembly / microtubule cytoskeleton organization involved in mitosis / E2F-enabled inhibition of pre-replication complex formation / G2/M DNA replication checkpoint / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / MASTL Facilitates Mitotic Progression / Activation of NIMA Kinases NEK9, NEK6, NEK7 / mitotic nuclear membrane disassembly / : / Phosphorylation of Emi1 / cyclin A2-CDK1 complex / Transcriptional regulation by RUNX2 / Phosphorylation of the APC/C / Nuclear Pore Complex (NPC) Disassembly / meiosis I / 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 / Golgi Cisternae Pericentriolar Stack Reorganization / cyclin-dependent protein serine/threonine kinase activator activity / Condensation of Prometaphase Chromosomes / chromosome condensation / [RNA-polymerase]-subunit kinase / centrosome cycle / cyclin-dependent protein serine/threonine kinase regulator activity / SCF ubiquitin ligase complex / response to copper ion / MAPK3 (ERK1) activation / response to amine / cyclin-dependent protein kinase activity / G1/S-Specific Transcription / mitotic G2 DNA damage checkpoint signaling / Regulation of APC/C activators between G1/S and early anaphase / regulation of embryonic development / peptidyl-threonine phosphorylation / protein deubiquitination / positive regulation of G2/M transition of mitotic cell cycle / response to cadmium ion / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / response to axon injury / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Cyclin A/B1/B2 associated events during G2/M transition / positive regulation of cardiac muscle cell proliferation / cyclin-dependent protein kinase holoenzyme complex / ERK1 and ERK2 cascade / Hsp70 protein binding / epithelial cell differentiation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / RNA polymerase II CTD heptapeptide repeat kinase activity / APC/C:Cdc20 mediated degradation of Cyclin B / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / cyclin binding / regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / AURKA Activation by TPX2 / Condensation of Prophase Chromosomes / positive regulation of DNA replication / ubiquitin binding / response to activity / spindle microtubule / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / G1/S transition of mitotic cell cycle / MAPK6/MAPK4 signaling / regulation of circadian rhythm / PKR-mediated signaling / peptidyl-serine phosphorylation / positive regulation of protein import into nucleus / response to toxic substance / positive regulation of protein localization to nucleus / microtubule cytoskeleton organization / G2/M transition of mitotic cell cycle / cellular response to hydrogen peroxide / The role of GTSE1 in G2/M progression after G2 checkpoint / mitotic spindle / Ovarian tumor domain proteases / kinase activity / rhythmic process / Regulation of TP53 Degradation / Regulation of PLK1 Activity at G2/M Transition / cell migration / virus receptor activity / protein-containing complex assembly / fibroblast proliferation / midbody
Similarity search - Function
Cyclin-Dependent Kinase Subunit Type 2 / Cyclin-dependent kinase, regulatory subunit / 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 / : / Phosphorylase Kinase; domain 1 ...Cyclin-Dependent Kinase Subunit Type 2 / Cyclin-dependent kinase, regulatory subunit / 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 / : / 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-FB8 / Cyclin-dependent kinases regulatory subunit / Cyclin-dependent kinase 1 / Cyclin-dependent kinases regulatory subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsWood, D.J. / Korolchuk, S. / Tatum, N.J. / Wang, L.Z. / Endicott, J.A. / Noble, M.E.M. / Martin, M.P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N009738/1 United Kingdom
Cancer Research UKC2115/A21421 United Kingdom
CitationJournal: Cell Chem Biol / Year: 2019
Title: Differences in the Conformational Energy Landscape of CDK1 and CDK2 Suggest a Mechanism for Achieving Selective CDK Inhibition.
Authors: Wood, D.J. / Korolchuk, S. / Tatum, N.J. / Wang, L.Z. / Endicott, J.A. / Noble, M.E.M. / Martin, M.P.
History
DepositionJun 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclin-dependent kinase 1
B: Cyclin-dependent kinases regulatory subunit 2
C: Cyclin-dependent kinase 1
D: Cyclin-dependent kinases regulatory subunit 2
E: Cyclin-dependent kinase 1
F: Cyclin-dependent kinases regulatory subunit 2
G: Cyclin-dependent kinase 1
H: Cyclin-dependent kinases regulatory subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,7509
Polymers179,3798
Non-polymers3711
Water23413
1
A: Cyclin-dependent kinase 1
B: Cyclin-dependent kinases regulatory subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2163
Polymers44,8452
Non-polymers3711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-6 kcal/mol
Surface area18950 Å2
MethodPISA
2
C: Cyclin-dependent kinase 1
D: Cyclin-dependent kinases regulatory subunit 2


Theoretical massNumber of molelcules
Total (without water)44,8452
Polymers44,8452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-7 kcal/mol
Surface area19090 Å2
MethodPISA
3
E: Cyclin-dependent kinase 1
F: Cyclin-dependent kinases regulatory subunit 2


Theoretical massNumber of molelcules
Total (without water)44,8452
Polymers44,8452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-7 kcal/mol
Surface area18930 Å2
MethodPISA
4
G: Cyclin-dependent kinase 1
H: Cyclin-dependent kinases regulatory subunit 2


Theoretical massNumber of molelcules
Total (without water)44,8452
Polymers44,8452
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-7 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.995, 149.202, 87.260
Angle α, β, γ (deg.)90.00, 92.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34553.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK1, CDC2, CDC28A, CDKN1, P34CDC2 / Plasmid: pVL1393 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P06493, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein
Cyclin-dependent kinases regulatory subunit 2 / CKS-2


Mass: 10290.819 Da / Num. of mol.: 4
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, UniProt: K9J4F7*PLUS
#3: Chemical ChemComp-FB8 / 4-(2-methyl-3-propan-2-yl-imidazol-4-yl)-~{N}-(4-methylsulfonylphenyl)pyrimidin-2-amine


Mass: 371.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21N5O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.75→87.35 Å / Num. obs: 45022 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.8
Reflection shellResolution: 2.75→87.35 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.4 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YC6

4yc6


Resolution: 2.75→87.35 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.892 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2737 2187 4.9 %RANDOM
Rwork0.22691 ---
obs0.2292 42835 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 73.119 Å2
Baniso -1Baniso -2Baniso -3
1-2.38 Å2-0 Å2-0.28 Å2
2---3.06 Å2-0 Å2
3---0.7 Å2
Refinement stepCycle: 1 / Resolution: 2.75→87.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11742 0 26 13 11781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01912072
X-RAY DIFFRACTIONr_bond_other_d00.0211361
X-RAY DIFFRACTIONr_angle_refined_deg1.541.97216324
X-RAY DIFFRACTIONr_angle_other_deg3.6532.99826390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26751416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15523.464563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.603152196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0861581
X-RAY DIFFRACTIONr_chiral_restr0.0870.21751
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113065
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022483
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_it5.1297.1955697
X-RAY DIFFRACTIONr_mcbond_other5.1257.1955696
X-RAY DIFFRACTIONr_mcangle_it8.01810.7797102
X-RAY DIFFRACTIONr_mcangle_other8.01910.7797103
X-RAY DIFFRACTIONr_scbond_it4.9957.5696375
X-RAY DIFFRACTIONr_scbond_other4.9947.5696376
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.02911.1639223
X-RAY DIFFRACTIONr_long_range_B_refined11.67580.36112862
X-RAY DIFFRACTIONr_long_range_B_other11.67580.36312863
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 145 -
Rwork0.348 3161 -
obs--99.34 %

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