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Yorodumi- PDB-4mq2: The crystal structure of DYRK1a with a bound pyrido[2,3-d]pyrimid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mq2 | ||||||
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Title | The crystal structure of DYRK1a with a bound pyrido[2,3-d]pyrimidine inhibitor | ||||||
Components | Dual specificity tyrosine-phosphorylation-regulated kinase 1ADYRK1A | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / dyrk1a / dyrk1b / kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of mRNA splicing, via spliceosome / negative regulation of DNA damage response, signal transduction by p53 class mediator ...histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of mRNA splicing, via spliceosome / negative regulation of DNA damage response, signal transduction by p53 class mediator / amyloid-beta formation / G0 and Early G1 / peptidyl-tyrosine autophosphorylation / cytoskeletal protein binding / protein serine/threonine/tyrosine kinase activity / tubulin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / positive regulation of RNA splicing / peptidyl-threonine phosphorylation / tau protein binding / non-membrane spanning protein tyrosine kinase activity / circadian rhythm / peptidyl-tyrosine phosphorylation / : / nervous system development / actin binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / protein autophosphorylation / transcription coactivator activity / cytoskeleton / protein kinase activity / nuclear speck / ribonucleoprotein complex / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Lukacs, C.M. / Janson, C.A. / Garvie, C. / Liang, L. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2013 Title: Pyrido[2,3-d]pyrimidines: Discovery and preliminary SAR of a novel series of DYRK1B and DYRK1A inhibitors. Authors: Anderson, K. / Chen, Y. / Chen, Z. / Dominique, R. / Glenn, K. / He, Y. / Janson, C. / Luk, K.C. / Lukacs, C. / Polonskaia, A. / Qiao, Q. / Railkar, A. / Rossman, P. / Sun, H. / Xiang, Q. / ...Authors: Anderson, K. / Chen, Y. / Chen, Z. / Dominique, R. / Glenn, K. / He, Y. / Janson, C. / Luk, K.C. / Lukacs, C. / Polonskaia, A. / Qiao, Q. / Railkar, A. / Rossman, P. / Sun, H. / Xiang, Q. / Vilenchik, M. / Wovkulich, P. / Zhang, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mq2.cif.gz | 287.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mq2.ent.gz | 233.4 KB | Display | PDB format |
PDBx/mmJSON format | 4mq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/4mq2 ftp://data.pdbj.org/pub/pdb/validation_reports/mq/4mq2 | HTTPS FTP |
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-Related structure data
Related structure data | 4mq1C 2vx3S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 42081.535 Da / Num. of mol.: 4 / Fragment: UNP residues 127-485 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK1A, DYRK, MNB, MNBH / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: Q13627, dual-specificity kinase #2: Chemical | ChemComp-2C4 / #3: Chemical | ChemComp-1PE / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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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: 3.21 Å3/Da / Density % sol: 61.64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 15% PEG 300, 0.1M LiSO4, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 3, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 53115 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 73 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 8.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2vx3 Resolution: 2.8→36.78 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.899 / SU B: 12.571 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.784 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.443 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→36.78 Å
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Refine LS restraints |
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