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Yorodumi- PDB-1ke5: CDK2 complexed with N-methyl-4-{[(2-oxo-1,2-dihydro-3H-indol-3-yl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ke5 | ||||||
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Title | CDK2 complexed with N-methyl-4-{[(2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]amino}benzenesulfonamide | ||||||
Components | Cell division protein kinase 2 | ||||||
Keywords | TRANSFERASE / cyclin kinase | ||||||
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: 2.2 Å | ||||||
Authors | Bramson, H.N. / Corona, J. / Davis, S.T. / Dickerson, S.H. / Edelstein, M. / Frye, S.V. / Gampe, R.T. / Hassell, A.M. / Shewchuk, L.M. / Kuyper, L.F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2001 Title: Oxindole-based inhibitors of cyclin-dependent kinase 2 (CDK2): design, synthesis, enzymatic activities, and X-ray crystallographic analysis. Authors: Bramson, H.N. / Corona, J. / Davis, S.T. / Dickerson, S.H. / Edelstein, M. / Frye, S.V. / Gampe Jr., R.T. / Harris, P.A. / Hassell, A. / Holmes, W.D. / Hunter, R.N. / Lackey, K.E. / Lovejoy, ...Authors: Bramson, H.N. / Corona, J. / Davis, S.T. / Dickerson, S.H. / Edelstein, M. / Frye, S.V. / Gampe Jr., R.T. / Harris, P.A. / Hassell, A. / Holmes, W.D. / Hunter, R.N. / Lackey, K.E. / Lovejoy, B. / Luzzio, M.J. / Montana, V. / Rocque, W.J. / Rusnak, D. / Shewchuk, L. / Veal, J.M. / Walker, D.H. / Kuyper, L.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ke5.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ke5.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ke5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ke5_validation.pdf.gz | 681.6 KB | Display | wwPDB validaton report |
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Full document | 1ke5_full_validation.pdf.gz | 688.7 KB | Display | |
Data in XML | 1ke5_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 1ke5_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/1ke5 ftp://data.pdbj.org/pub/pdb/validation_reports/ke/1ke5 | HTTPS FTP |
-Related 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): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24941, EC: 2.7.1.37 |
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#2: Chemical | ChemComp-LS1 / |
#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: 2.13 Å3/Da / Density % sol: 42.21 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG3340, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Details: Shewchuk L., (2000) J. Med. Chem., 43, 133. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 23, 1998 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 15271 / Num. obs: 13376 / % possible obs: 87.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2.2→2.34 Å / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 15.5 / % possible all: 90.6 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 500 Å / Num. measured all: 51192 / Rmerge(I) obs: 0.043 |
Reflection shell | *PLUS Rmerge(I) obs: 0.082 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.12 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016
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Refinement | *PLUS Lowest resolution: 8 Å / Rfactor obs: 0.184 / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.184 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.236 / Rfactor Rwork: 0.192 |