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Yorodumi- PDB-2v22: REPLACE: A strategy for Iterative Design of Cyclin Binding Groove... -
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-Basic information
Entry | Database: PDB / ID: 2v22 | ||||||
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Title | REPLACE: A strategy for Iterative Design of Cyclin Binding Groove Inhibitors | ||||||
Components |
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Keywords | TRANSFERASE / POLYMORPHISM / CYCLIN GROOVE / CELL DIVISION / CDK2 / KINASE / CYCLIN / ACTIVE / MITOSIS / INHIBITION / PHOSPHORYLATION / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / CELL CYCLE / NONPEPTIDE / ATP-BINDING | ||||||
Function / homology | Function and homology information G2 Phase / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cyclin A2-CDK2 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / p53-Dependent G1 DNA Damage Response / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Regulation of APC/C activators between G1/S and early anaphase ...G2 Phase / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cyclin A2-CDK2 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / p53-Dependent G1 DNA Damage Response / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Regulation of APC/C activators between G1/S and early anaphase / cellular response to leptin stimulus / male pronucleus / Telomere Extension By Telomerase / G0 and Early G1 / female pronucleus / response to glucagon / cellular response to cocaine / cellular response to nitric oxide / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / positive regulation of DNA biosynthetic process / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cochlea development / cellular response to platelet-derived growth factor stimulus / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / regulation of DNA replication / animal organ regeneration / post-translational protein modification / cellular response to estradiol stimulus / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Orc1 removal from chromatin / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / Regulation of TP53 Degradation / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / Ras protein signal transduction / Ub-specific processing proteases / protein domain specific binding / cell division / centrosome / DNA-templated transcription / positive regulation of DNA-templated transcription / protein kinase binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Andrews, M.J. / Kontopidis, G. / McInnes, C. / Plater, A. / Innes, L. / Cowan, A. / Jewsbury, P. / Fischer, P.M. | ||||||
Citation | Journal: Chembiochem / Year: 2006 Title: Replace: A Strategy for Iterative Design of Cyclin- Binding Groove Inhibitors Authors: Andrews, M.J. / Kontopidis, G. / Mcinnes, C. / Plater, A. / Innes, L. / Cowan, A. / Jewsbury, P. / Fischer, P.M. #1: Journal: Chem.Biol. / Year: 2006 Title: Differential Binding of Inhibitors to Active and Inactive Cdk2 Provides Insights for Drug Design Authors: Kontopidis, G. / Mcinnes, C. / Pandalaneni, S.R. / Mcnae, I. / Gibson, D. / Mezna, M. / Thomas, M. / Wood, G. / Wang, S. / Walkinshaw, M.D. / Fische, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v22.cif.gz | 243.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v22.ent.gz | 197.2 KB | Display | PDB format |
PDBx/mmJSON format | 2v22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v22_validation.pdf.gz | 992.5 KB | Display | wwPDB validaton report |
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Full document | 2v22_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2v22_validation.xml.gz | 48.6 KB | Display | |
Data in CIF | 2v22_validation.cif.gz | 67.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/2v22 ftp://data.pdbj.org/pub/pdb/validation_reports/v2/2v22 | HTTPS FTP |
-Related structure data
Related structure data | 2uueC 1ol1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / End auth comp-ID: LEU / End label comp-ID: LEU
NCS ensembles :
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-Components
#1: Protein | Mass: 33976.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: TRIAZOL-1-METHYL-PYRIMIDIN INHIBITOR / Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P24941, EC: 2.7.1.37 #2: Protein | Mass: 29753.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CAP-TETRAPEPTIDE INHIBITOR / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P20248 #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 7.8 / Details: 22% PEG 3350, 0.1M NA3-CIT, pH 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 14, 2003 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 126787 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.6→2.74 Å / Rmerge(I) obs: 1.06 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OL1 Resolution: 2.6→16 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.889 / SU B: 12.366 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 1.815 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAIN A AND C RESIDUES 12-17, 37-41, 159-162
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→16 Å
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Refine LS restraints |
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