+Open data
-Basic information
Entry | Database: PDB / ID: 6q3b | ||||||
---|---|---|---|---|---|---|---|
Title | CDK2 in complex with FragLite2 | ||||||
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 / 4-IODOPYRAZOLE / Uncharacterized protein Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å | ||||||
Authors | Wood, D.J. / Martin, M.P. / Noble, M.E.M. | ||||||
Funding support | United Kingdom, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6q3b.cif.gz | 139 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6q3b.ent.gz | 106.9 KB | Display | PDB format |
PDBx/mmJSON format | 6q3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q3b_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6q3b_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6q3b_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 6q3b_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/6q3b ftp://data.pdbj.org/pub/pdb/validation_reports/q3/6q3b | HTTPS FTP |
-Related structure data
Related structure data | 6q3cC 6q3fC 6q48C 6q49C 6q4aC 6q4bC 6q4cC 6q4dC 6q4eC 6q4fC 6q4gC 6q4hC 6q4iC 6q4jC 6q4kC 1hckS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.69 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting 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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.916 Å / Relative weight: 1 |
Reflection | Resolution: 1.11→72.34 Å / Num. obs: 110033 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.11→1.13 Å / Redundancy: 6.5 % / Rmerge(I) obs: 2.54 / Mean I/σ(I) obs: 0.4 / CC1/2: 0.35 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HCK Resolution: 1.11→42.92 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.044 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.881 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.11→42.92 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|