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Yorodumi- PDB-1pxo: HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR [4-(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pxo | ||||||
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Title | HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR [4-(2-Amino-4-methyl-thiazol-5-yl)-pyrimidin-2-yl]-(3-nitro-phenyl)-amine | ||||||
Components | Cell division protein kinase 2 | ||||||
Keywords | TRANSFERASE / PROTEIN KINASE / CELL CYCLE / PHOSPHORYLATION / CELL DIVISION / MITOSIS / INHIBITION / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / 3D-STRUCTURE. | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Wang, S. / Meades, C. / Wood, G. / Osnowski, A. / Anderson, S. / Yuill, R. / Thomas, M. / Mezna, M. / Jackson, W. / Midgley, C. ...Wang, S. / Meades, C. / Wood, G. / Osnowski, A. / Anderson, S. / Yuill, R. / Thomas, M. / Mezna, M. / Jackson, W. / Midgley, C. / Griffiths, G. / McNae, I. / Wu, S.Y. / McInnes, C. / Zheleva, D. / Walkinshaw, M.D. / Fischer, P.M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2004 Title: 2-Anilino-4-(thiazol-5-yl)pyrimidine CDK inhibitors: synthesis, SAR analysis, X-ray crystallography, and biological activity. Authors: Wang, S. / Meades, C. / Wood, G. / Osnowski, A. / Anderson, S. / Yuill, R. / Thomas, M. / Mezna, M. / Jackson, W. / Midgley, C. / Griffiths, G. / Fleming, I. / Green, S. / McNae, I. / Wu, S. ...Authors: Wang, S. / Meades, C. / Wood, G. / Osnowski, A. / Anderson, S. / Yuill, R. / Thomas, M. / Mezna, M. / Jackson, W. / Midgley, C. / Griffiths, G. / Fleming, I. / Green, S. / McNae, I. / Wu, S.Y. / McInnes, C. / Zheleva, D. / Walkinshaw, M.D. / Fischer, P.M. #1: Journal: Structure / Year: 2003 Title: Discovery of a novel family of CDK inhibitors with the program LIDAEUS: structural basis for ligand-induced disordering of the activation loop. Authors: Wu, S.Y. / McNae, I. / Kontopidis, G. / McClue, S.J. / McInnes, C. / Stewart, K.J. / Wang, S. / Zheleva, D.I. / Marriage, H. / Lane, D.P. / Taylor, P. / Fischer, P.M. / Walkinshaw, M.D. | ||||||
History |
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Remark 600 | HETEROGEN partial CK7 500 has alternate conformation with HOH 501,502,503,504,505,506,507,508,and 509. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pxo.cif.gz | 78.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pxo.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 1pxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pxo_validation.pdf.gz | 973 KB | Display | wwPDB validaton report |
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Full document | 1pxo_full_validation.pdf.gz | 987.6 KB | Display | |
Data in XML | 1pxo_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 1pxo_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/1pxo ftp://data.pdbj.org/pub/pdb/validation_reports/px/1pxo | HTTPS FTP |
-Related structure data
Related structure data | 1pxmC 1pxnC 1pxpC 1hclS 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) / Gene: CDK2 / Cell line (production host): Hi5 / 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-CK7 / [ |
#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: 2.05 Å3/Da / Density % sol: 39.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: PEG 6000, NA-HEPES, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→15 Å / Num. obs: 20604 / % possible obs: 99.4 % / Redundancy: 10.97 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.96→2.07 Å / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 7.7 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HCL Resolution: 1.96→14.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1664384.74 / Data cutoff high rms absF: 1664384.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 74.2328 Å2 / ksol: 0.399945 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.96→14.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.07 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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