HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound SCM

Identifiers

  • Canonical SMILES: 
    CN[C@@H]1[C@H](O)[C@H](NC)[C@H]2O[C@]3(O)[C@@H](O[C@H](C)CC3=O)O[C@@H]2[C@H]1O
  • IUPAC name: 
    (2R,4aR,5aR,6S,7S,8R,9S,9aR,10aS)-4a,7,9-trihydroxy-2-methyl-6,8-bis(methylamino)decahydro-4H-pyrano[2,3-b][1,4]benzodioxin-4-one
  • InChi: 
    InChI=1S/C14H24N2O7/c1-5-4-6(17)14(20)13(21-5)22-12-10(19)7(15-2)9(18)8(16-3)11(12)23-14/h5,7-13,15-16,18-20H,4H2,1-3H3/t5-,7-,8+,9+,10+,11-,12-,13+,14+/m1/s1
  • InChiKey: 
    UNFWWIHTNXNPBV-WXKVUWSESA-N
  • SMARTS: 
    [#6]-[#7]-[#6@@H]1-[#6@H](-[#8])-[#6@H](-[#7]-[#6])-[#6@H]2-[#8]-[#6@]3(-[#8])-[#6@@H](-[#8]-[#6@H](-[#6])-[#6]-[#6]-3=[#8])-[#8]-[#6@@H]-2-[#6@H]-1-[#8]

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

15541 CHEMBL1167 DB00919

RNA-SM complexes

PDB code Deposition date Reference publication
1fjg Aug. 8, 2000 Carter Andrew P., Clemons William M., Brodersen Ditlev E., Morgan-Warren Robert J., Wimberly Brian T., Ramakrishnan V.. . Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics Nature
28uh Feb. 20, 2026 Steinmetzger Christian, Karlsson Hampus, Fontana Carolina, Galindo Riera Natalia, Riad Magdalena, Kosek David, Schlagnitweit Judith, Steiner Emilie, Sandoz Sarah Friebe, Andersson Emma R., Petzold Katja. . Universal 3D Motif dynamics in RNA: The A-minor Switch []
28ui Feb. 20, 2026 Steinmetzger Christian, Karlsson Hampus, Fontana Carolina, Galindo Riera Natalia, Riad Magdalena, Kosek David, Schlagnitweit Judith, Steiner Emilie, Sandoz Sarah Friebe, Andersson Emma R., Petzold Katja. . Universal 3D Motif dynamics in RNA: The A-minor Switch []
28uj Feb. 20, 2026 Steinmetzger Christian, Karlsson Hampus, Fontana Carolina, Galindo Riera Natalia, Riad Magdalena, Kosek David, Schlagnitweit Judith, Steiner Emilie, Sandoz Sarah Friebe, Andersson Emma R., Petzold Katja. . Universal 3D Motif dynamics in RNA: The A-minor Switch []
28uk Feb. 20, 2026 Steinmetzger Christian, Karlsson Hampus, Fontana Carolina, Galindo Riera Natalia, Riad Magdalena, Kosek David, Schlagnitweit Judith, Steiner Emilie, Sandoz Sarah Friebe, Andersson Emma R., Petzold Katja. . Universal 3D Motif dynamics in RNA: The A-minor Switch []
28ul Feb. 20, 2026 Steinmetzger Christian, Karlsson Hampus, Fontana Carolina, Galindo Riera Natalia, Riad Magdalena, Kosek David, Schlagnitweit Judith, Steiner Emilie, Sandoz Sarah Friebe, Andersson Emma R., Petzold Katja. . Universal 3D Motif dynamics in RNA: The A-minor Switch []
28um Feb. 20, 2026 Steinmetzger Christian, Karlsson Hampus, Fontana Carolina, Galindo Riera Natalia, Riad Magdalena, Kosek David, Schlagnitweit Judith, Steiner Emilie, Sandoz Sarah Friebe, Andersson Emma R., Petzold Katja. . Universal 3D Motif dynamics in RNA: The A-minor Switch []
28un Feb. 20, 2026 Steinmetzger Christian, Karlsson Hampus, Fontana Carolina, Galindo Riera Natalia, Riad Magdalena, Kosek David, Schlagnitweit Judith, Steiner Emilie, Sandoz Sarah Friebe, Andersson Emma R., Petzold Katja. . Universal 3D Motif dynamics in RNA: The A-minor Switch []
4v56 July 21, 2007 Borovinskaya Maria A., Shoji Shinichiro, Holton James M., Fredrick Kurt, Cate Jamie H. D.. . A Steric Block in Translation Caused by the Antibiotic Spectinomycin ACS Chemical Biology
4v56 July 21, 2007 Borovinskaya Maria A., Shoji Shinichiro, Holton James M., Fredrick Kurt, Cate Jamie H. D.. . A Steric Block in Translation Caused by the Antibiotic Spectinomycin ACS Chemical Biology
4v57 July 21, 2007 Borovinskaya Maria A., Shoji Shinichiro, Holton James M., Fredrick Kurt, Cate Jamie H. D.. . A Steric Block in Translation Caused by the Antibiotic Spectinomycin ACS Chemical Biology
4v57 July 21, 2007 Borovinskaya Maria A., Shoji Shinichiro, Holton James M., Fredrick Kurt, Cate Jamie H. D.. . A Steric Block in Translation Caused by the Antibiotic Spectinomycin ACS Chemical Biology
7n2v May 29, 2021 Rundlet Emily J., Holm Mikael, Schacherl Magdalena, Natchiar S. Kundhavai, Altman Roger B., Spahn Christian M. T., Myasnikov Alexander G., Blanchard Scott C.. . Structural basis of early translocation events on the ribosome Nature
7n2v May 29, 2021 Rundlet Emily J., Holm Mikael, Schacherl Magdalena, Natchiar S. Kundhavai, Altman Roger B., Spahn Christian M. T., Myasnikov Alexander G., Blanchard Scott C.. . Structural basis of early translocation events on the ribosome Nature
7n2v May 29, 2021 Rundlet Emily J., Holm Mikael, Schacherl Magdalena, Natchiar S. Kundhavai, Altman Roger B., Spahn Christian M. T., Myasnikov Alexander G., Blanchard Scott C.. . Structural basis of early translocation events on the ribosome Nature
7p7q July 20, 2021 Crowe-McAuliffe Caillan, Murina Victoriia, Turnbull Kathryn Jane, Huch Susanne, Kasari Marje, Takada Hiraku, Nersisyan Lilit, Sundsfjord Arnfinn, Hegstad Kristin, Atkinson Gemma C., Pelechano Vicent, Wilson Daniel N., Hauryliuk Vasili. . Structural basis for PoxtA-mediated resistance to phenicol and oxazolidinone antibiotics Nature Communications
7p7r July 20, 2021 Crowe-McAuliffe Caillan, Murina Victoriia, Turnbull Kathryn Jane, Huch Susanne, Kasari Marje, Takada Hiraku, Nersisyan Lilit, Sundsfjord Arnfinn, Hegstad Kristin, Atkinson Gemma C., Pelechano Vicent, Wilson Daniel N., Hauryliuk Vasili. . Structural basis for PoxtA-mediated resistance to phenicol and oxazolidinone antibiotics Nature Communications
7p7s July 20, 2021 Crowe-McAuliffe Caillan, Murina Victoriia, Turnbull Kathryn Jane, Huch Susanne, Kasari Marje, Takada Hiraku, Nersisyan Lilit, Sundsfjord Arnfinn, Hegstad Kristin, Atkinson Gemma C., Pelechano Vicent, Wilson Daniel N., Hauryliuk Vasili. . Structural basis for PoxtA-mediated resistance to phenicol and oxazolidinone antibiotics Nature Communications
7p7t July 20, 2021 Crowe-McAuliffe Caillan, Murina Victoriia, Turnbull Kathryn Jane, Huch Susanne, Kasari Marje, Takada Hiraku, Nersisyan Lilit, Sundsfjord Arnfinn, Hegstad Kristin, Atkinson Gemma C., Pelechano Vicent, Wilson Daniel N., Hauryliuk Vasili. . Structural basis for PoxtA-mediated resistance to phenicol and oxazolidinone antibiotics Nature Communications
7p7u July 20, 2021 Crowe-McAuliffe Caillan, Murina Victoriia, Turnbull Kathryn Jane, Huch Susanne, Kasari Marje, Takada Hiraku, Nersisyan Lilit, Sundsfjord Arnfinn, Hegstad Kristin, Atkinson Gemma C., Pelechano Vicent, Wilson Daniel N., Hauryliuk Vasili. . Structural basis for PoxtA-mediated resistance to phenicol and oxazolidinone antibiotics Nature Communications
7pib Aug. 19, 2021 Xue Liang, Lenz Swantje, Zimmermann-Kogadeeva Maria, Tegunov Dimitry, Cramer Patrick, Bork Peer, Rappsilber Juri, Mahamid Julia. . Visualizing translation dynamics at atomic detail inside a bacterial cell Nature
8ca7 Jan. 24, 2023 Paternoga Helge, Crowe-McAuliffe Caillan, Bock Lars V., Koller Timm O., Morici Martino, Beckert Bertrand, Myasnikov Alexander G., Grubmüller Helmut, Nováček Jiří, Wilson Daniel N.. . Structural conservation of antibiotic interaction with ribosomes Nature Structural & Molecular Biology
8cai Jan. 24, 2023 Paternoga Helge, Crowe-McAuliffe Caillan, Bock Lars V., Koller Timm O., Morici Martino, Beckert Bertrand, Myasnikov Alexander G., Grubmüller Helmut, Nováček Jiří, Wilson Daniel N.. . Structural conservation of antibiotic interaction with ribosomes Nature Structural & Molecular Biology
8uvr Nov. 3, 2023 Phelps Gregory A., Cheramie Martin N., Fernando Dinesh M., Selchow Petra, Meyer Christopher J., Waidyarachchi Samanthi L., Dharuman Suresh, Liu Jiuyu, Meuli Michael, Molin Michael Dal, Killam Benjamin Y., Murphy Patricia A., Reeve Stephanie M., Wilt Laura A., Anderson Shelby M., Yang Lei, Lee Robin B., Temrikar Zaid H., Lukka Pradeep B., Meibohm Bernd, Polikanov Yury S., Hobbie Sven N., Böttger Erik C., Sander Peter, Lee Richard E.. . Development of 2nd generation aminomethyl spectinomycins that overcome native efflux in Mycobacterium abscessus Proceedings of the National Academy of Sciences
8uvr Nov. 3, 2023 Phelps Gregory A., Cheramie Martin N., Fernando Dinesh M., Selchow Petra, Meyer Christopher J., Waidyarachchi Samanthi L., Dharuman Suresh, Liu Jiuyu, Meuli Michael, Molin Michael Dal, Killam Benjamin Y., Murphy Patricia A., Reeve Stephanie M., Wilt Laura A., Anderson Shelby M., Yang Lei, Lee Robin B., Temrikar Zaid H., Lukka Pradeep B., Meibohm Bernd, Polikanov Yury S., Hobbie Sven N., Böttger Erik C., Sander Peter, Lee Richard E.. . Development of 2nd generation aminomethyl spectinomycins that overcome native efflux in Mycobacterium abscessus Proceedings of the National Academy of Sciences
9h90 Oct. 29, 2024 Raulf Karoline, Koller Timm O, Beckert Bertrand, Lepak Alexander, Morici Martino, Mardirossian Mario, Scocchi Marco, Bange Gert, Wilson Daniel N. . The structure of the Vibrio natriegens 70S ribosome in complex with the proline-rich antimicrobial peptide Bac5(1–17) Nucleic Acids Research
9tmi Dec. 13, 2025 Steinmetzger Christian, Karlsson Hampus, Fontana Carolina, Galindo Riera Natalia, Riad Magdalena, Kosek David, Schlagnitweit Judith, Steiner Emilie, Sandoz Sarah Friebe, Andersson Emma R., Petzold Katja. . Universal 3D Motif dynamics in RNA: The A-minor Switch []
9tnl Dec. 16, 2025 Steinmetzger Christian, Karlsson Hampus, Fontana Carolina, Galindo Riera Natalia, Riad Magdalena, Kosek David, Schlagnitweit Judith, Steiner Emilie, Sandoz Sarah Friebe, Andersson Emma R., Petzold Katja. . Universal 3D Motif dynamics in RNA: The A-minor Switch []
9tqa Dec. 19, 2025 Steinmetzger Christian, Karlsson Hampus, Fontana Carolina, Galindo Riera Natalia, Riad Magdalena, Kosek David, Schlagnitweit Judith, Steiner Emilie, Sandoz Sarah Friebe, Andersson Emma R., Petzold Katja. . Universal 3D Motif dynamics in RNA: The A-minor Switch []

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 332.16 g/mol
HBA 9
HBD 5
HBA + HBD
AlogP -2.93
TPSA 129.51
RB 2

Radar chart