+Open data
-Basic information
Entry | Database: PDB / ID: 5anq | ||||||
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Title | inhibitors of JumonjiC domain-containing histone demethylases | ||||||
Components | LYSINE-SPECIFIC DEMETHYLASE 4A | ||||||
Keywords | OXIDOREDUCTASE / EPIGENETICS / HISTONE DEMETHYLASES / INHIBITORS / JUMONJIC DOMAIN / VIRTUAL SCREENING | ||||||
Function / homology | Function and homology information [histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / positive regulation of neuron differentiation / response to nutrient levels / negative regulation of autophagy / HDMs demethylate histones / fibrillar center / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Roatsch, M. / Robaa, D. / Pippel, M. / Nettleship, J.E. / Reddivari, Y. / Bird, L.E. / Hoffmann, I. / Franz, H. / Owens, R.J. / Schuele, R. ...Roatsch, M. / Robaa, D. / Pippel, M. / Nettleship, J.E. / Reddivari, Y. / Bird, L.E. / Hoffmann, I. / Franz, H. / Owens, R.J. / Schuele, R. / Flaig, R. / Sippl, W. / Jung, M. | ||||||
Citation | Journal: Fut.Med.Chem. / Year: 2016 Title: Substituted 2-(2-Aminopyrimidin-4-Yl)Pyridine-4-Carboxylates as Potent Inhibitors of Jumonjic Domain-Containing Histone Demethylases. Authors: Roatsch, M. / Robaa, D. / Pippel, M. / Nettleship, J.E. / Reddivari, Y. / Bird, L.E. / Hoffmann, I. / Franz, H. / Owens, R.J. / Schole, R. / Flaig, R. / Sippl, W. / Jung, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5anq.cif.gz | 161.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5anq.ent.gz | 128.4 KB | Display | PDB format |
PDBx/mmJSON format | 5anq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5anq_validation.pdf.gz | 996.9 KB | Display | wwPDB validaton report |
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Full document | 5anq_full_validation.pdf.gz | 999.6 KB | Display | |
Data in XML | 5anq_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 5anq_validation.cif.gz | 42.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/5anq ftp://data.pdbj.org/pub/pdb/validation_reports/an/5anq | HTTPS FTP |
-Related structure data
Related structure data | 2ox0S S: Starting model for refinement |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41767.543 Da / Num. of mol.: 2 / Fragment: JMJN, JMJC, RESIDUES 1-359 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS References: UniProt: O75164, [histone H3]-dimethyl-L-lysine36 demethylase |
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-Non-polymers , 6 types, 365 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | ChemComp-CL / #7: 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: 2.59 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | Details: 0.233 M LITHIUM SULFATE, 24% PEG 3350, 0.1 M HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2014 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→49.76 Å / Num. obs: 59001 / % possible obs: 99 % / Observed criterion σ(I): 1.2 / Redundancy: 4.5 % / Biso Wilson estimate: 43.7 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.15 / Mean I/σ(I) obs: 1.2 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OX0 Resolution: 2→49.76 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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: 46.636 Å2
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Refinement step | Cycle: LAST / Resolution: 2→49.76 Å
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