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- PDB-5nev: CDK2/Cyclin A in complex with compound 73 -

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Basic information

Entry
Database: PDB / ID: 5nev
TitleCDK2/Cyclin A in complex with compound 73
Components
  • Cyclin-A2
  • Cyclin-dependent kinase 2
KeywordsTRANSFERASE / CDK2 CYCLIN A / CDK2 SELECTIVE TRANSFERASE
Function / homology
Function and homology information


Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine ...Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / positive regulation of DNA biosynthetic process / cochlea development / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cellular response to platelet-derived growth factor stimulus / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / 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 / regulation of DNA replication / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / Cajal body / cyclin-dependent kinase / animal organ regeneration / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / meiotic cell cycle / positive regulation of DNA replication / male germ cell nucleus / response to organic substance / cellular response to estradiol stimulus / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / G1/S transition of mitotic cell cycle / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Meiotic recombination / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / cellular response to hypoxia / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / Ras protein signal transduction / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / DNA replication / chromosome, telomeric region / Ub-specific processing proteases / endosome / chromatin remodeling / cell division / protein domain specific binding / protein phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA-templated transcription / positive regulation of cell population proliferation / protein kinase binding / positive regulation of DNA-templated transcription
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-like ...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-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-72L / Cyclin-A2 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsCoxon, C.R. / Anscombe, E. / Harnor, S.J. / Martin, M.P. / Carbain, B. / Hardcastle, I.R. / Harlow, L.K. / Korolchuk, S. / Matheson, C.J. / Noble, M.E.M. ...Coxon, C.R. / Anscombe, E. / Harnor, S.J. / Martin, M.P. / Carbain, B. / Hardcastle, I.R. / Harlow, L.K. / Korolchuk, S. / Matheson, C.J. / Noble, M.E.M. / Newell, D.R. / Turner, D. / Sivaprakasam, M. / Wang, L.Z. / Wong, C. / Golding, B.T. / Griffin, R.J. / Cano, G.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Cyclin-Dependent Kinase (CDK) Inhibitors: Structure-Activity Relationships and Insights into the CDK-2 Selectivity of 6-Substituted 2-Arylaminopurines.
Authors: Coxon, C.R. / Anscombe, E. / Harnor, S.J. / Martin, M.P. / Carbain, B. / Golding, B.T. / Hardcastle, I.R. / Harlow, L.K. / Korolchuk, S. / Matheson, C.J. / Newell, D.R. / Noble, M.E. / ...Authors: Coxon, C.R. / Anscombe, E. / Harnor, S.J. / Martin, M.P. / Carbain, B. / Golding, B.T. / Hardcastle, I.R. / Harlow, L.K. / Korolchuk, S. / Matheson, C.J. / Newell, D.R. / Noble, M.E. / Sivaprakasam, M. / Tudhope, S.J. / Turner, D.M. / Wang, L.Z. / Wedge, S.R. / Wong, C. / Griffin, R.J. / Endicott, J.A. / Cano, C.
History
DepositionMar 12, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionMar 29, 2017ID: 5LQE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Cyclin-dependent kinase 2
D: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,5906
Polymers128,7054
Non-polymers8852
Water28816
1
A: Cyclin-dependent kinase 2
B: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7953
Polymers64,3532
Non-polymers4421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-18 kcal/mol
Surface area23400 Å2
MethodPISA
2
C: Cyclin-dependent kinase 2
D: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7953
Polymers64,3532
Non-polymers4421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-19 kcal/mol
Surface area23500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.527, 132.053, 149.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPROAA0 - 2945 - 299
21SERSERPROPROCC0 - 2945 - 299
12VALVALTHRTHRBB175 - 4293 - 257
22VALVALTHRTHRDD175 - 4293 - 257

NCS ensembles :
ID
1
2

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Components

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


Mass: 34467.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P24941, cyclin-dependent kinase
#2: Protein Cyclin-A2 / Cyclin-A / Cyclin A


Mass: 29884.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNA2, CCN1, CCNA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20248
#3: Chemical ChemComp-72L / 4-[[6-(3-phenylphenyl)-7~{H}-purin-2-yl]amino]benzenesulfonamide


Mass: 442.493 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H18N6O2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.81 Å3/Da / Density % sol: 56.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PROTEIN AT 5MG PER ML. 0.6 TO 0.8M KCL, 0.9 TO 1.2M (NH402SO4, AND 100MM HEPES (PH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.97→66.03 Å / Num. obs: 30773 / % possible obs: 100 % / Redundancy: 704 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 6.7
Reflection shellResolution: 2.97→3.13 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H1S

1h1s


Resolution: 2.97→66.03 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.908 / SU B: 52.79 / SU ML: 0.423 / Cross valid method: THROUGHOUT / ESU R Free: 0.438 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26119 1544 5 %RANDOM
Rwork0.21767 ---
obs0.21992 29173 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 80.244 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0 Å2-0 Å2
2---1.63 Å20 Å2
3---2.05 Å2
Refinement stepCycle: 1 / Resolution: 2.97→66.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8886 0 64 16 8966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0199182
X-RAY DIFFRACTIONr_bond_other_d0.0020.028677
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.98212471
X-RAY DIFFRACTIONr_angle_other_deg1.3412.99620146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08651099
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.24623.929392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.442151604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1161544
X-RAY DIFFRACTIONr_chiral_restr0.1070.21400
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219915
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021831
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_it0.6291.2954412
X-RAY DIFFRACTIONr_mcbond_other0.6291.2954413
X-RAY DIFFRACTIONr_mcangle_it1.1451.9425505
X-RAY DIFFRACTIONr_mcangle_other1.1451.9415506
X-RAY DIFFRACTIONr_scbond_it0.541.3184770
X-RAY DIFFRACTIONr_scbond_other0.541.3184771
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9711.966967
X-RAY DIFFRACTIONr_long_range_B_refined2.61214.73210177
X-RAY DIFFRACTIONr_long_range_B_other2.61214.73110178
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A187240.07
12C187240.07
21B170420.05
22D170420.05
LS refinement shellResolution: 2.97→3.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 110 -
Rwork0.337 2135 -
obs--100 %
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)
13.3951-0.9791-1.90453.22650.15693.1330.0005-0.2596-0.21620.44530.1164-0.2792-0.23940.3684-0.11690.0895-0.0216-0.07890.630.00290.5459-5.788-25.74310.031
22.05660.56270.67933.43360.69673.42630.00920.34250.3448-0.26710.03380.0415-0.54780.1251-0.04310.26980.0270.05260.57940.08430.517-20.9341.079-1.627
33.6817-0.3566-0.96543.6902-0.60382.0484-0.3045-0.29180.00990.37650.30840.364-0.2464-0.5584-0.00380.87240.04180.0890.8632-0.18520.6329-47.28711.52233.434
44.42710.09360.04544.9015-1.2032.8193-0.34720.0281-0.73760.0670.23470.93830.6908-0.60880.11251.0515-0.22590.37520.7071-0.13310.8885-42.617-21.335.016
50.89911.6242-1.88842.9625-3.42663.97540.1871-0.0865-0.1610.5235-0.429-0.2315-0.61890.26570.24190.57010.1349-0.66221.3049-0.73331.0425-18.818-3.72728.324
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 295
2X-RAY DIFFRACTION2B175 - 429
3X-RAY DIFFRACTION3C0 - 296
4X-RAY DIFFRACTION4D175 - 429
5X-RAY DIFFRACTION5E1 - 2

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