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Yorodumi- PDB-2c68: Crystal structure of the human CDK2 complexed with the triazolopy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c68 | |||||||||
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Title | Crystal structure of the human CDK2 complexed with the triazolopyrimidine inhibitor | |||||||||
Components | CELL DIVISION PROTEIN KINASE 2 | |||||||||
Keywords | TRANSFERASE / SERINE/THREONINE PROTEIN KINASE / CDK2 / ATP-BINDING / CELL CYCLE / MITOSIS / PHOSPHORYLATION / TRIAZOLOPYRIMIDINE INHIBITOR / CELL DIVISION / KINASE / POLYMORPHISM / NUCLEOTIDE-BINDING | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Richardson, C.M. / Dokurno, P. / Murray, J.B. / Surgenor, A.E. | |||||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: Triazolo[1,5-A]Pyrimidines as Novel Cdk2 Inhibitors: Protein Structure-Guided Design and Sar. Authors: Richardson, C.M. / Williamson, D.S. / Parratt, M.J. / Borgognoni, J. / Cansfield, A.D. / Dokurno, P. / Francis, G.L. / Howes, R. / Moore, J.D. / Murray, J.B. / Robertson, A. / 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 | 2c68.cif.gz | 81.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c68.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 2c68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c68_validation.pdf.gz | 793.2 KB | Display | wwPDB validaton report |
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Full document | 2c68_full_validation.pdf.gz | 799.9 KB | Display | |
Data in XML | 2c68_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 2c68_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/2c68 ftp://data.pdbj.org/pub/pdb/validation_reports/c6/2c68 | HTTPS FTP |
-Related structure data
Related structure data | 2c69C 2c6iC 2c6kC 2c6lC 2c6mC 2c6oC 2c6tC 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) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P24941, EC: 2.7.1.37 |
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#2: Chemical | ChemComp-CT6 / ( |
#3: Water | ChemComp-HOH / |
Compound details | INVOLVED IN THE CONTROL OF THE CELL CYCLE. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.7 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG3350, HEPES PH 7.2, AMMONIUM ACETATE, VAPOR DIFFUSION HANGING DROP, ROOM TEMPERATURE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Apr 8, 2003 / Details: MIRRORS |
Radiation | Monochromator: MSC OSMIC BLUE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→35 Å / Num. obs: 20039 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.9 / % possible all: 96.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B39 Resolution: 1.95→15 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.365 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.191 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→15 Å
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Refine LS restraints |
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