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Open data
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Basic information
Entry | Database: PDB / ID: 4uv8 | ||||||
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Title | LSD1(KDM1A)-CoREST in complex with 1-Benzyl-Tranylcypromine | ||||||
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![]() | TRANSCRIPTION / COVALENT INHIBITOR | ||||||
Function / homology | ![]() positive regulation of megakaryocyte differentiation / guanine metabolic process / regulation of DNA methylation-dependent heterochromatin formation / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development ...positive regulation of megakaryocyte differentiation / guanine metabolic process / regulation of DNA methylation-dependent heterochromatin formation / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development / neuron maturation / positive regulation of neural precursor cell proliferation / regulation of androgen receptor signaling pathway / MRF binding / DNA repair complex / DNA repair-dependent chromatin remodeling / nuclear androgen receptor binding / regulation of double-strand break repair via homologous recombination / positive regulation of neuroblast proliferation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of stem cell proliferation / negative regulation of DNA binding / histone H3K9 demethylase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase complex / positive regulation of cell size / histone demethylase activity / positive regulation of epithelial to mesenchymal transition / cellular response to cAMP / response to fungicide / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription repressor complex / erythrocyte differentiation / nuclear receptor coactivator activity / negative regulation of protein binding / positive regulation of protein ubiquitination / Regulation of PTEN gene transcription / HDACs deacetylate histones / promoter-specific chromatin binding / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / negative regulation of DNA-binding transcription factor activity / cellular response to gamma radiation / cerebral cortex development / positive regulation of neuron projection development / transcription corepressor activity / regulation of protein localization / cellular response to UV / p53 binding / chromatin organization / positive regulation of cold-induced thermogenesis / flavin adenine dinucleotide binding / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription factor binding / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / Potential therapeutics for SARS / chromosome, telomeric region / transcription coactivator activity / oxidoreductase activity / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vianello, P. / Botrugno, O. / Cappa, A. / Ciossani, G. / Dessanti, P. / Mai, A. / Mattevi, A. / Meroni, G. / Minucci, S. / Thaler, F. ...Vianello, P. / Botrugno, O. / Cappa, A. / Ciossani, G. / Dessanti, P. / Mai, A. / Mattevi, A. / Meroni, G. / Minucci, S. / Thaler, F. / Tortorici, M. / Trifiro, P. / Valente, S. / Villa, M. / Varasi, M. / Mercurio, C. | ||||||
![]() | ![]() Title: Synthesis, Biological Activity and Mechanistic Insights of 1-Substituted Cyclopropylamine Derivatives: A Novel Class of Irreversible Inhibitors of Histone Demethylase Kdm1A. Authors: Vianello, P. / Botrugno, O.A. / Cappa, A. / Ciossani, G. / Dessanti, P. / Mai, A. / Mattevi, A. / Meroni, G. / Minucci, S. / Thaler, F. / Tortorici, M. / Trifiro, P. / Valente, S. / Villa, M. ...Authors: Vianello, P. / Botrugno, O.A. / Cappa, A. / Ciossani, G. / Dessanti, P. / Mai, A. / Mattevi, A. / Meroni, G. / Minucci, S. / Thaler, F. / Tortorici, M. / Trifiro, P. / Valente, S. / Villa, M. / Varasi, M. / Mercurio, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.2 KB | Display | ![]() |
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PDB format | ![]() | 137.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4uv9C ![]() 4uvaC ![]() 4uvbC ![]() 4uvcC ![]() 2v1dS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 94846.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 53101.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-D69 / [[( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.27 Å3/Da / Density % sol: 75 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→60 Å / Num. obs: 62089 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.5 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2V1D Resolution: 2.8→58.96 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.959 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES - REFINED INDIVIDUALLY
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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: 81.222 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→58.96 Å
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