+Open data
-Basic information
Entry | Database: PDB / ID: 6q4j | |||||||||
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Title | CDK2 in complex with FragLite34 | |||||||||
Components | Cyclin-dependent kinase 2 | |||||||||
Keywords | CELL CYCLE / Fragment / FragLite / CDK2 / inhibitor | |||||||||
Function / homology | Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Protein kinase domain / 2-[3-(pyrimidin-4-ylamino)phenyl]ethanoic acid / Uncharacterized protein Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å | |||||||||
Authors | Wood, D.J. / Martin, M.P. / Noble, M.E.M. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: J.Med.Chem. / Year: 2019 Title: FragLites-Minimal, Halogenated Fragments Displaying Pharmacophore Doublets. An Efficient Approach to Druggability Assessment and Hit Generation. Authors: Wood, D.J. / Lopez-Fernandez, J.D. / Knight, L.E. / Al-Khawaldeh, I. / Gai, C. / Lin, S. / Martin, M.P. / Miller, D.C. / Cano, C. / Endicott, J.A. / Hardcastle, I.R. / Noble, M.E.M. / Waring, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q4j.cif.gz | 151.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q4j.ent.gz | 117.5 KB | Display | PDB format |
PDBx/mmJSON format | 6q4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q4j_validation.pdf.gz | 458.5 KB | Display | wwPDB validaton report |
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Full document | 6q4j_full_validation.pdf.gz | 468.2 KB | Display | |
Data in XML | 6q4j_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 6q4j_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/6q4j ftp://data.pdbj.org/pub/pdb/validation_reports/q4/6q4j | HTTPS FTP |
-Related structure data
Related structure data | 6q3bC 6q3cC 6q3fC 6q48C 6q49C 6q4aC 6q4bC 6q4cC 6q4dC 6q4eC 6q4fC 6q4gC 6q4hC 6q4iC 6q4kC 1hckS 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: 34761.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P24941, cyclin-dependent kinase | ||||
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#2: Chemical | #3: Chemical | ChemComp-HHB / | #4: 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: 1.99 Å3/Da / Density % sol: 38.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 10MG/ML CDK2 10% V/V PEG3350, 50 MM HEPES/NAOH, 50 MM NA/K PHOSPHATE, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→50.99 Å / Num. obs: 106937 / % possible obs: 82.9 % / Redundancy: 5.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.041 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.05→1.07 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.861 / Mean I/σ(I) obs: 1 / Num. unique obs: 5281 / CC1/2: 0.34 / % possible all: 6.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HCK Resolution: 1.05→50.99 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.035 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.701 Å2
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Refinement step | Cycle: 1 / Resolution: 1.05→50.99 Å
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Refine LS restraints |
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