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Yorodumi- PDB-5idn: CDK8-CYCC IN COMPLEX WITH [(S)-2-(4-Chloro-phenyl)-pyrrolidin-1-y... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5idn | ||||||
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Title | CDK8-CYCC IN COMPLEX WITH [(S)-2-(4-Chloro-phenyl)-pyrrolidin-1-yl]-(3-methyl-1H-pyrazolo[3,4-b]pyridin-5-yl)-methanone | ||||||
Components |
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Keywords | TRANSFERASE / CDK8 KINASE / CYCLIN C | ||||||
Function / homology | Function and homology information CKM complex / negative regulation of triglyceride metabolic process / G0 to G1 transition / mediator complex / Generic Transcription Pathway / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / negative regulation of Notch signaling pathway / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase ...CKM complex / negative regulation of triglyceride metabolic process / G0 to G1 transition / mediator complex / Generic Transcription Pathway / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / negative regulation of Notch signaling pathway / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / ubiquitin ligase complex / RNA polymerase II CTD heptapeptide repeat kinase activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PPARA activates gene expression / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Transcriptional regulation of white adipocyte differentiation / ubiquitin protein ligase activity / protein ubiquitination / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.26 Å | ||||||
Authors | Musil, D. / Blagg, J. / Mallinger, A. / Czodrowski, P. / Schiemann, K. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2016 Title: Structure-Based Optimization of Potent, Selective, and Orally Bioavailable CDK8 Inhibitors Discovered by High-Throughput Screening. Authors: Czodrowski, P. / Mallinger, A. / Wienke, D. / Esdar, C. / Poschke, O. / Busch, M. / Rohdich, F. / Eccles, S.A. / Ortiz-Ruiz, M.J. / Schneider, R. / Raynaud, F.I. / Clarke, P.A. / Musil, D. / ...Authors: Czodrowski, P. / Mallinger, A. / Wienke, D. / Esdar, C. / Poschke, O. / Busch, M. / Rohdich, F. / Eccles, S.A. / Ortiz-Ruiz, M.J. / Schneider, R. / Raynaud, F.I. / Clarke, P.A. / Musil, D. / Schwarz, D. / Dale, T. / Urbahns, K. / Blagg, J. / Schiemann, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5idn.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5idn.ent.gz | 111.8 KB | Display | PDB format |
PDBx/mmJSON format | 5idn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/5idn ftp://data.pdbj.org/pub/pdb/validation_reports/id/5idn | HTTPS FTP |
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-Related structure data
Related structure data | 5icpC 5idpC 4f6sS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 43247.066 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 3-405 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK8 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P49336, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase |
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#2: Protein | Mass: 31656.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24863 |
-Non-polymers , 4 types, 195 molecules
#3: Chemical | ChemComp-6A7 / [( | ||
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#4: Chemical | ChemComp-EDO / | ||
#5: Chemical | ChemComp-FMT / #6: 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: 3.1 Å3/Da / Density % sol: 59.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 20% PEG 3350, 0.2 M sodium formate, pH 6.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→84.01 Å / Num. obs: 40902 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.26→2.51 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.504 / % possible all: 97.8 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4F6S Resolution: 2.26→84.01 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.383 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.208 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.236 Å2
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Refinement step | Cycle: LAST / Resolution: 2.26→84.01 Å
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