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| <!DOCTYPE html><html><head><meta name='viewport' content='width=device-width, initial-scale=1'><meta name="description" content="A bioinformatic tool for identifying novel redox-active disulphide bonds in mammalian proteins, utilizing RCSB protein databank structures and providing a redox score."><meta name="keywords" content="ReDisulphID, bioinformatics, protein function, redox-active disulphides, covalent drugs, mammalian proteins, RCSB protein databank, redox score, HSE, solvent accessibility, pKa, disulphide bond prediction"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="robots" content="index, follow"><link rel='icon' type='image/png' href='icon.png'><link rel = 'stylesheet' href = 'style.css'><script src="jquery-3.7.1.min.js"></script><script src='3Dmol-min.js'></script><title>ReDisulphID</title></head><body><a href = 'list.html'><div class= 'title'>ReDisulphID<div class='subtitle'><p>a tool for identifying drug-targetable redox-active disulphides</div></div></a><div class = 'main'> | ||
| <div class = 'menu'><a class = 'button' href = 'index.html'><div class= 'menuitem'>Home</div></a><a class = 'button' href = 'about.html'><div class= 'menuitem'>About</div></a><a class = 'button' href = 'list.html'><div class= 'menuitem'>List</div></a></div><h1>Transferrin receptor protein 1</h1><div class = 'tabs'><div class = 'sep'>Intramolecular</div><a href = '#0' class = 'tablink'><div class = 'item' style='background:rgba(147.84322820037107,255,100,0.4);'>Cysteine 354 and cysteine 364</div></a></div><div class = 'tab'><div class = 'item structure' style='background:rgba(200, 200, 200, 0.4);;'><p class = 'struc' hidden>6s9j E 353 E 363 </p> <div style='height: 100%; position: relative;' class='viewer_3Dmoljs viewer' data-backgroundcolor='0xffffff' data-style='stick' data-ui='false'></div></div><div class = 'item redoxstatement' style='background:rgba(147.84322820037107,255,100,0.4);'>A redox-regulated disulphide may form within <b>Transferrin receptor protein 1</b> between cysteines 354 and 364 (353 and 363 respectively in this structure). </div><h2>Details</h2><div class = 'grid'><div class = 'item infotitle'>Redox score <a title = 'The redox score is related to how likely a cysteine pair is to form a redox active disulphide. It is calculated from solvent accessibility, pKa, and distance between each thiol in the cysteine pair. The highest redox score is 100.0, and the lowest redox score of a known redox-active intermolecular disulphide is 60, while the lowest score overall is 0.' href = 'about.html#scoreinfo'>?</a></div><div class = 'item info'>86</div><div class = 'item infotitle'>PDB code</div><a class = 'link' target='_blank' rel='noopener' href = 'https://www.rcsb.org/structure/6s9j' ><div class = 'item info'>6s9j</div></a><div class = 'item infotitle'>Structure name</div><div class = 'item info'>crystal structure of tfr1 mimicry in complex with gp1 from macv</div><div class = 'item infotitle'>Structure deposition date </div><div class = 'item info'>2019-07-15</div><div class = 'item infotitle'>Thiol separation (Å)</div><div class = 'item info'>2</div><div class = 'item infotitle'>Half-sphere exposure sum <a title = 'HSE is a measure of the accessibility of an amino acid side-chain. Cα atoms are counted in a 12 Å radius around the Cα of each cysteine in the potential redox-active disulphide bond. A lower HSE means an amino acid has fewer proximal amino acids, so is more accessible.' href = 'about.html#hseinfo'>?</a></div><div class = 'item info'>61</div><div class = 'item infotitle'>Minimum pK<sub>a</sub> <a title = 'The lowest pKa from each thiol in the cystiene pair. A lower minimum pKa means a cysteine pair is more likely to form a redox-regulated disulphide bond. The pKa of the cysteine thiols in the potential redox-active disulphide bond are calculated using the PROPKA algorithm.' href = 'about.html#pkainfo'>?</a></div><div class = 'item info'>nan</div><div class = 'item infotitle'>% buried</div><div class = 'item info'>nan</div><div class = 'item infotitle'>Peptide accession</div><a class = 'link' target='_blank' rel='noopener' href = 'https://www.uniprot.org/uniprotkb/A0A060BIS8/entry'><div class = 'item info'>A0A060BIS8</div></a><div class = 'item infotitle'>Residue number A</div><div class = 'item info'>354</div><div class = 'item infotitle'>Residue number B</div><div class = 'item info'>364</div><div class = 'item infotitle'>Peptide name</div><div class = 'item info'>Transferrin receptor protein 1</div></div><h2>Ligandability</h2><h3>Cysteine 353 of Transferrin receptor protein 1</h3><div class = 'grid'><div class = 'item ligandability '><p><a href = 'https://pubs.acs.org/doi/10.1021/jacs.1c11053' target='_blank' rel='noopener'>Not ligandable in the dataset of Yang <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cbic.202000870' target='_blank' rel='noopener'>Not ligandable in the dataset of Yan <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://www.nature.com/articles/nature18002' target='_blank' rel='noopener'>Not ligandable in the dataset of Backus <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://doi.org/10.1016/j.cell.2020.07.001' target='_blank' rel='noopener'>Not ligandable in the dataset of Vinogradova <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://doi.org/10.1021/acs.analchem.0c04726' target='_blank' rel='noopener'>Not ligandable in the dataset of Cao <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://www.nature.com/articles/s41587-020-00778-3' target='_blank' rel='noopener'>Not ligandable in the dataset of Kuljanin <i>et al.</i></a></p></div></div><h3>Cysteine 363 of Transferrin receptor protein 1</h3><div class = 'grid'><div class = 'item ligandability '><p><a href = 'https://pubs.acs.org/doi/10.1021/jacs.1c11053' target='_blank' rel='noopener'>Not ligandable in the dataset of Yang <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cbic.202000870' target='_blank' rel='noopener'>Not ligandable in the dataset of Yan <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://www.nature.com/articles/nature18002' target='_blank' rel='noopener'>Not ligandable in the dataset of Backus <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://doi.org/10.1016/j.cell.2020.07.001' target='_blank' rel='noopener'>Not ligandable in the dataset of Vinogradova <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://doi.org/10.1021/acs.analchem.0c04726' target='_blank' rel='noopener'>Not ligandable in the dataset of Cao <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://www.nature.com/articles/s41587-020-00778-3' target='_blank' rel='noopener'>Not ligandable in the dataset of Kuljanin <i>et al.</i></a></p></div></div></div><div class = 'citation'>If this tool was useful for finding a disulphide, please cite: <p></div></div><script src='search.js'></script></body></html> | ||
| <div class = 'menu'><a class = 'button' href = 'index.html'><div class= 'menuitem'>Home</div></a><a class = 'button' href = 'about.html'><div class= 'menuitem'>About</div></a><a class = 'button' href = 'list.html'><div class= 'menuitem'>List</div></a></div><h1>Transferrin receptor protein 1</h1><div class = 'tabs'><div class = 'sep'>Intramolecular</div><a href = '#0' class = 'tablink'><div class = 'item' style='background:rgba(147.84322820037107,255,100,0.4);'>Cysteine 354 and cysteine 364</div></a></div><div class = 'tab'><div class = 'item structure' style='background:rgba(200, 200, 200, 0.4);;'><p class = 'struc' hidden>6s9j E 353 E 363 </p> <div style='height: 100%; position: relative;' class='viewer_3Dmoljs viewer' data-backgroundcolor='0xffffff' data-style='stick' data-ui='false'></div></div><div class = 'item redoxstatement' style='background:rgba(147.84322820037107,255,100,0.4);'>A redox-regulated disulphide may form within <b>Transferrin receptor protein 1</b> between cysteines 354 and 364 (353 and 363 respectively in this structure). </div><h2>Details</h2><div class = 'grid'><div class = 'item infotitle'>Redox score <a title = 'The redox score is related to how likely a cysteine pair is to form a redox active disulphide. It is calculated from solvent accessibility, pKa, and distance between each thiol in the cysteine pair. The highest redox score is 100.0, and the lowest redox score of a known redox-active intermolecular disulphide is 60, while the lowest score overall is 0.' href = 'about.html#scoreinfo'>?</a></div><div class = 'item info'>86</div><div class = 'item infotitle'>PDB code</div><a class = 'link' target='_blank' rel='noopener' href = 'https://www.rcsb.org/structure/6s9j' ><div class = 'item info'>6s9j</div></a><div class = 'item infotitle'>Structure name</div><div class = 'item info'>crystal structure of tfr1 mimicry in complex with gp1 from macv</div><div class = 'item infotitle'>Structure deposition date </div><div class = 'item info'>2019-07-15</div><div class = 'item infotitle'>Thiol separation (Å)</div><div class = 'item info'>2</div><div class = 'item infotitle'>Half-sphere exposure sum <a title = 'HSE is a measure of the accessibility of an amino acid side-chain. Cα atoms are counted in a 12 Å radius around the Cα of each cysteine in the potential redox-active disulphide bond. A lower HSE means an amino acid has fewer proximal amino acids, so is more accessible.' href = 'about.html#hseinfo'>?</a></div><div class = 'item info'>61</div><div class = 'item infotitle'>Minimum pK<sub>a</sub> <a title = 'The lowest pKa from each thiol in the cystiene pair. A lower minimum pKa means a cysteine pair is more likely to form a redox-regulated disulphide bond. The pKa of the cysteine thiols in the potential redox-active disulphide bond are calculated using the PROPKA algorithm.' href = 'about.html#pkainfo'>?</a></div><div class = 'item info'>nan</div><div class = 'item infotitle'>% buried</div><div class = 'item info'>nan</div><div class = 'item infotitle'>Peptide accession</div><a class = 'link' target='_blank' rel='noopener' href = 'https://www.uniprot.org/uniprotkb/A0A060BIS8/entry'><div class = 'item info'>A0A060BIS8</div></a><div class = 'item infotitle'>Residue number A</div><div class = 'item info'>354</div><div class = 'item infotitle'>Residue number B</div><div class = 'item info'>364</div><div class = 'item infotitle'>Peptide name</div><div class = 'item info'>Transferrin receptor protein 1</div></div><h2>Ligandability</h2><h3>Cysteine 354 of Transferrin receptor protein 1</h3><div class = 'grid'><div class = 'item ligandability '><p><a href = 'https://pubs.acs.org/doi/10.1021/jacs.1c11053' target='_blank' rel='noopener'>Not ligandable in the dataset of Yang <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cbic.202000870' target='_blank' rel='noopener'>Not ligandable in the dataset of Yan <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://www.nature.com/articles/nature18002' target='_blank' rel='noopener'>Not ligandable in the dataset of Backus <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://doi.org/10.1016/j.cell.2020.07.001' target='_blank' rel='noopener'>Not ligandable in the dataset of Vinogradova <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://doi.org/10.1021/acs.analchem.0c04726' target='_blank' rel='noopener'>Not ligandable in the dataset of Cao <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://www.nature.com/articles/s41587-020-00778-3' target='_blank' rel='noopener'>Not ligandable in the dataset of Kuljanin <i>et al.</i></a></p></div></div><h3>Cysteine 364 of Transferrin receptor protein 1</h3><div class = 'grid'><div class = 'item ligandability '><p><a href = 'https://pubs.acs.org/doi/10.1021/jacs.1c11053' target='_blank' rel='noopener'>Not ligandable in the dataset of Yang <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cbic.202000870' target='_blank' rel='noopener'>Not ligandable in the dataset of Yan <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://www.nature.com/articles/nature18002' target='_blank' rel='noopener'>Not ligandable in the dataset of Backus <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://doi.org/10.1016/j.cell.2020.07.001' target='_blank' rel='noopener'>Not ligandable in the dataset of Vinogradova <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://doi.org/10.1021/acs.analchem.0c04726' target='_blank' rel='noopener'>Not ligandable in the dataset of Cao <i>et al.</i></a></p></div><div class = 'item ligandability '><p><a href = 'https://www.nature.com/articles/s41587-020-00778-3' target='_blank' rel='noopener'>Not ligandable in the dataset of Kuljanin <i>et al.</i></a></p></div></div></div><div class = 'citation'>If this tool was useful for finding a disulphide, please cite: <p></div></div><script src='search.js'></script></body></html> |
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