+Open data
-Basic information
Entry | Database: PDB / ID: 1r78 | ||||||
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Title | CDK2 complex with a 4-alkynyl oxindole inhibitor | ||||||
Components | Cell division protein kinase 2 | ||||||
Keywords | TRANSFERASE / cyclin dependent kinase / serine/threonine protein kinase / oxindole | ||||||
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 / rigid body refinement / Resolution: 2 Å | ||||||
Authors | Luk, K.-C. / Simcox, M.E. / Schutt, A. / Rowan, K. / Thompson, T. / Chen, Y. / Kammlott, U. / DePinto, W. / Dunten, P. / Dermatakis, A. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2004 Title: A new series of potent oxindole inhibitors of CDK2 Authors: Luk, K.-C. / Simcox, M.E. / Schutt, A. / Rowan, K. / Thompson, T. / Chen, Y. / Kammlott, U. / DePinto, W. / Dunten, P. / Dermatakis, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r78.cif.gz | 68.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r78.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 1r78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r78_validation.pdf.gz | 461.6 KB | Display | wwPDB validaton report |
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Full document | 1r78_full_validation.pdf.gz | 464.7 KB | Display | |
Data in XML | 1r78_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 1r78_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r7/1r78 ftp://data.pdbj.org/pub/pdb/validation_reports/r7/1r78 | HTTPS FTP |
-Related structure data
Related structure data | |
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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) / Gene: CDK2 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P24941, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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#2: Chemical | ChemComp-FMD / |
#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: 2.08 Å3/Da / Density % sol: 40.73 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 9 / Details: pH 9, VAPOR DIFFUSION, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 6, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 18512 / Num. obs: 18512 / % possible obs: 93.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.036 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.05 / % possible all: 69.1 |
-Processing
Software |
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Refinement | Method to determine structure: rigid body refinement / Resolution: 2→51.3 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.883 / SU B: 4.407 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 21.889 Å2
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Refinement step | Cycle: LAST / Resolution: 2→51.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.048 Å / Total num. of bins used: 20
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Refinement | *PLUS Highest resolution: 2 Å / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.234 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |