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Yorodumi- PDB-2uzo: Crystal structure of human CDK2 complexed with a thiazolidinone i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uzo | ||||||
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Title | Crystal structure of human CDK2 complexed with a thiazolidinone inhibitor | ||||||
Components | CELL DIVISION PROTEIN KINASE 2 | ||||||
Keywords | TRANSFERASE / ATP-BINDING / PHOSPHORYLATION / CDK2 / KINASE / CYCLIN / MITOSIS / CELL CYCLE / CELL DIVISION / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / THIAZOLIDINONE LIGAND | ||||||
Function / homology | Function and homology information Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich ...Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Richardson, C.M. / Dokurno, P. / Murray, J.B. / Surgenor, A.E. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2007 Title: Discovery of a Potent Cdk2 Inhibitor with a Novel Binding Mode, Using Virtual Screening and Initial, Structure-Guided Lead Scoping. Authors: Richardson, C.M. / Nunns, C.L. / Williamson, D.S. / Parratt, M.J. / Dokurno, P. / Howes, R. / Borgognoni, J. / Drysdale, M.J. / Finch, H. / Hubbard, R.E. / Jackson, P.S. / Kierstan, P. / ...Authors: Richardson, C.M. / Nunns, C.L. / Williamson, D.S. / Parratt, M.J. / Dokurno, P. / Howes, R. / Borgognoni, J. / Drysdale, M.J. / Finch, H. / Hubbard, R.E. / Jackson, P.S. / Kierstan, P. / Lentzen, G. / Moore, J.D. / Murray, J.B. / Simmonite, H. / Surgenor, A.E. / Torrance, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uzo.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uzo.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 2uzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uzo_validation.pdf.gz | 696.8 KB | Display | wwPDB validaton report |
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Full document | 2uzo_full_validation.pdf.gz | 703.2 KB | Display | |
Data in XML | 2uzo_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 2uzo_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/2uzo ftp://data.pdbj.org/pub/pdb/validation_reports/uz/2uzo | HTTPS FTP |
-Related structure data
Related structure data | 2uzbC 2uzdC 2uzeC 2uzlC 2uznC 2v0dC 1b39S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33976.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF21 References: UniProt: P24941, cyclin-dependent kinase, EC: 2.7.1.37 |
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#2: Chemical | ChemComp-C62 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: VAPOR DIFFUSION HANGING DROP, ROOM TEMPERATURE, PEG3350, HEPES PH7.2, AMMONIUM ACETATE, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 19, 2003 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 14029 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B39 Resolution: 2.3→12 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.873 / SU B: 7.911 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.556 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→12 Å
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Refine LS restraints |
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