+Open data
-Basic information
Entry | Database: PDB / ID: 4dhf | ||||||
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Title | Structure of Aurora A mutant bound to Biogenidec cpd 15 | ||||||
Components | Aurora kinase A | ||||||
Keywords | transferase/transferase inhibitor / Ser/Thr kinase mitotic kinase pyrazolopyrimidine / phosphorylation / TPX2 / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / meiotic spindle / mitotic centrosome separation / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / positive regulation of mitochondrial fission / spindle organization / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic cell cycle / AURKA Activation by TPX2 / mitotic spindle organization / positive regulation of mitotic nuclear division / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / ciliary basal body / negative regulation of protein binding / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / molecular function activator activity / liver regeneration / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / regulation of protein stability / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / mitotic spindle / kinetochore / spindle / response to wounding / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / microtubule / postsynaptic density / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / cell division / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Silvian, L. / Marcotte, D.J. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2012 Title: Structure-based design of 2,6,7-trisubstituted-7H-pyrrolo[2,3-d]pyrimidines as Aurora kinases inhibitors. Authors: Le Brazidec, J.Y. / Pasis, A. / Tam, B. / Boykin, C. / Wang, D. / Marcotte, D.J. / Claassen, G. / Chong, J.H. / Chao, J. / Fan, J. / Nguyen, K. / Silvian, L. / Ling, L. / Zhang, L. / Choi, M. ...Authors: Le Brazidec, J.Y. / Pasis, A. / Tam, B. / Boykin, C. / Wang, D. / Marcotte, D.J. / Claassen, G. / Chong, J.H. / Chao, J. / Fan, J. / Nguyen, K. / Silvian, L. / Ling, L. / Zhang, L. / Choi, M. / Teng, M. / Pathan, N. / Zhao, S. / Li, T. / Taveras, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dhf.cif.gz | 119.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dhf.ent.gz | 93.7 KB | Display | PDB format |
PDBx/mmJSON format | 4dhf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/4dhf ftp://data.pdbj.org/pub/pdb/validation_reports/dh/4dhf | HTTPS FTP |
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-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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31346.939 Da / Num. of mol.: 2 / Fragment: unp residues 126-391 / Mutation: T287D, T288D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: AIK, AIRK1, ARK1, AURA, AURKA, AuroraA, AYK1, BTAK, IAK1, STK15, STK6 Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: O14965, non-specific serine/threonine protein kinase #2: Chemical | #3: Chemical | #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.67 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 1mM ADP, 2mM MgCl2 addition and set up with 10% PEG550MME, 5% Ethylene glycol, 0.1M TRIS, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD |
Radiation | Monochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 15443 / Num. obs: 15344 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 20 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→27.68 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.881 / SU B: 17.433 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.401 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→27.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
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