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Yorodumi- PDB-2c6i: Crystal structure of the human CDK2 complexed with the triazolopy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c6i | ||||||
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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: 1.8 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 | 2c6i.cif.gz | 81.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c6i.ent.gz | 60.3 KB | Display | PDB format |
PDBx/mmJSON format | 2c6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c6i_validation.pdf.gz | 721.9 KB | Display | wwPDB validaton report |
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Full document | 2c6i_full_validation.pdf.gz | 727.2 KB | Display | |
Data in XML | 2c6i_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 2c6i_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/2c6i ftp://data.pdbj.org/pub/pdb/validation_reports/c6/2c6i | HTTPS FTP |
-Related structure data
Related structure data | 2c68C 2c69C 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-DT1 / |
#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: 2.09 Å3/Da / Density % sol: 40.71 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG3350, HEPES PH7.2, AMMONIUM ACETATE, VAPOR DIFFUSION HANGING DROP, ROOM TEMPERATURE, pH 7.20 |
-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 MSC / Detector: IMAGE PLATE / Date: Apr 23, 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: 1.8→30 Å / Num. obs: 25808 / % possible obs: 97 % / Redundancy: 2.92 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.8 / % possible all: 76.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B39 Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.803 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.171 / 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: 41.17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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