HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound SPM

Identifiers

  • Canonical SMILES: 
    NCCCNCCCCNCCCN
  • IUPAC name: 
    N,N'-bis(3-aminopropyl)butane-1,4-diamine
  • InChi: 
    InChI=1S/C10H26N4/c11-5-3-9-13-7-1-2-8-14-10-4-6-12/h13-14H,1-12H2
  • InChiKey: 
    PFNFFQXMRSDOHW-UHFFFAOYSA-N

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

1103 CHEMBL23194 DB00127

RNA-SM complexes

PDB code Deposition date Reference publication
7nsi March 7, 2021 Kummer Eva, Schubert Katharina Noel, Schoenhut Tanja, Scaiola Alain, Ban Nenad. . Structural basis of translation termination, rescue, and recycling in mammalian mitochondria Molecular Cell
8ifb Feb. 17, 2023 Tomono Junta, Asano Kosuke, Chiashi Takuma, Suzuki Masato, Igarashi Masayuki, Takahashi Yoshiaki, Tanaka Yoshikazu, Yokoyama Takeshi. . Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside The Journal of Biochemistry
8akn July 30, 2022 Koller Timm O., Morici Martino, Berger Max, Safdari Haaris A., Lele Deepti S., Beckert Bertrand, Kaur Kanwal J., Wilson Daniel N.. . Structural basis for translation inhibition by the glycosylated drosocin peptide Nature Chemical Biology
6rw4 June 3, 2019 Khawaja Anas, Itoh Yuzuru, Remes Cristina, Spåhr Henrik, Yukhnovets Olessya, Höfig Henning, Amunts Alexey, Rorbach Joanna. . Distinct pre-initiation steps in human mitochondrial translation Nature Communications
4e8m March 20, 2012 Marcia Marco, Pyle Anna Marie. . Visualizing Group II Intron Catalysis through the Stages of Splicing Cell
4r0d July 30, 2014 Robart Aaron R., Chan Russell T., Peters Jessica K., Rajashankar Kanagalaghatta R., Toor Navtej. . Crystal structure of a eukaryotic group II intron lariat Nature
4faq May 22, 2012 Marcia Marco, Pyle Anna Marie. . Visualizing Group II Intron Catalysis through the Stages of Splicing Cell
4e8k March 20, 2012 Marcia Marco, Pyle Anna Marie. . Visualizing Group II Intron Catalysis through the Stages of Splicing Cell
6gaz April 13, 2018 Kummer Eva, Leibundgut Marc, Rackham Oliver, Lee Richard G., Boehringer Daniel, Filipovska Aleksandra, Ban Nenad. . Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM Nature
7o7z April 14, 2021 Bhatt Pramod R., Scaiola Alain, Loughran Gary, Leibundgut Marc, Kratzel Annika, Meurs Romane, Dreos René, O’Connor Kate M., McMillan Angus, Bode Jeffrey W., Thiel Volker, Gatfield David, Atkins John F., Ban Nenad. . Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome Science
7qi4 Dec. 14, 2021 Singh Vivek, Itoh Yuzuru, Del’Olio Samuel, Hassan Asem, Naschberger Andreas, Flygaard Rasmus Kock, Nobe Yuko, Izumikawa Keiichi, Aibara Shintaro, Andréll Juni, Whitford Paul C, Barrientos Antoni, Taoka Masato, Amunts Alexey. . Structure of mitoribosome reveals mechanism of mRNA binding, tRNA interactions with L1 stalk, roles of cofactors and rRNA modifications []
4far May 22, 2012 Marcia Marco, Pyle Anna Marie. . Visualizing Group II Intron Catalysis through the Stages of Splicing Cell
7oaw April 20, 2021 Mieczkowski Mateusz, Steinmetzger Christian, Bessi Irene, Lenz Ann-Kathrin, Schmiedel Alexander, Holzapfel Marco, Lambert Christoph, Pena Vladimir, Höbartner Claudia. . Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine Nature Communications
1evv April 20, 2000 Jovine Luca, Djordjevic Snezana, Rhodes Daniela. . The crystal structure of yeast phenylalanine tRNA at 2.0 Å resolution: cleavage by Mg 2+ in 15-year old crystals 1 1Edited by J. Karn Journal of Molecular Biology
7oax April 20, 2021 Mieczkowski Mateusz, Steinmetzger Christian, Bessi Irene, Lenz Ann-Kathrin, Schmiedel Alexander, Holzapfel Marco, Lambert Christoph, Pena Vladimir, Höbartner Claudia. . Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine Nature Communications
7nqh March 1, 2021 Kummer Eva, Schubert Katharina Noel, Schoenhut Tanja, Scaiola Alain, Ban Nenad. . Structural basis of translation termination, rescue, and recycling in mammalian mitochondria Molecular Cell
4e8p March 20, 2012 Marcia Marco, Pyle Anna Marie. . Visualizing Group II Intron Catalysis through the Stages of Splicing Cell
1j8g May 21, 2001 Deng Junpeng, Xiong Yong, Sundaralingam Muttaiya. . X-ray analysis of an RNA tetraplex (UGGGGU) 4 with divalent Sr 2+ ions at subatomic resolution (0.61 Å) Proceedings of the National Academy of Sciences
5vj9 April 19, 2017 Reiss Caroline W., Strobel Scott A.. . Structural basis for ligand binding to the guanidine-II riboswitch RNA
4e8t March 20, 2012 Marcia Marco, Pyle Anna Marie. . Visualizing Group II Intron Catalysis through the Stages of Splicing Cell
8any Aug. 6, 2022
7o7y April 14, 2021 Bhatt Pramod R., Scaiola Alain, Loughran Gary, Leibundgut Marc, Kratzel Annika, Meurs Romane, Dreos René, O’Connor Kate M., McMillan Angus, Bode Jeffrey W., Thiel Volker, Gatfield David, Atkins John F., Ban Nenad. . Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome Science
7nsj March 7, 2021 Kummer Eva, Schubert Katharina Noel, Schoenhut Tanja, Scaiola Alain, Ban Nenad. . Structural basis of translation termination, rescue, and recycling in mammalian mitochondria Molecular Cell
8ana Aug. 5, 2022 Koller Timm O., Morici Martino, Berger Max, Safdari Haaris A., Lele Deepti S., Beckert Bertrand, Kaur Kanwal J., Wilson Daniel N.. . Structural basis for translation inhibition by the glycosylated drosocin peptide Nature Chemical Biology
1tn1 Dec. 4, 1986 Brown R. S., Dewan J. C., Klug A.. . Crystallographic and biochemical investigation of the lead(II)-catalyzed hydrolysis of yeast phenylalanine tRNA Biochemistry
6t3k Oct. 11, 2019 Manigrasso Jacopo, Chillón Isabel, Genna Vito, Vidossich Pietro, Somarowthu Srinivas, Pyle Anna Marie, De Vivo Marco, Marcia Marco. . Visualizing group II intron dynamics between the first and second steps of splicing Nature Communications
7k00 Sept. 2, 2020 Watson Zoe L, Ward Fred R, Méheust Raphaël, Ad Omer, Schepartz Alanna, Banfield Jillian F, Cate Jamie HD. . Structure of the bacterial ribosome at 2 Å resolution eLife
7p2e July 5, 2021 Itoh Yuzuru, Singh Vivek, Khawaja Anas, Naschberger Andreas, Nguyen Minh Duc, Rorbach Joanna, Amunts Alexey. . Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules eLife
7l0z Dec. 13, 2020 Jeng Sunny C.Y., Trachman Robert J., Weissenboeck Florian, Truong Lynda, Link Katie A., Jepsen Mette D.E., Knutson Jay R., Andersen Ebbe S., Ferré-D'Amaré Adrian R., Unrau Peter J.. . Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET RNA
7edt March 17, 2021
4far May 22, 2012 Marcia Marco, Pyle Anna Marie. . Visualizing Group II Intron Catalysis through the Stages of Splicing Cell
4e8q March 20, 2012 Marcia Marco, Pyle Anna Marie. . Visualizing Group II Intron Catalysis through the Stages of Splicing Cell
6rw5 June 3, 2019 Khawaja Anas, Itoh Yuzuru, Remes Cristina, Spåhr Henrik, Yukhnovets Olessya, Höfig Henning, Amunts Alexey, Rorbach Joanna. . Distinct pre-initiation steps in human mitochondrial translation Nature Communications
8auv Aug. 25, 2022 Smirnova Julia, Loerke Justus, Kleinau Gunnar, Schmidt Andrea, Bürger Jörg, Meyer Etienne H., Mielke Thorsten, Scheerer Patrick, Bock Ralph, Spahn Christian M. T., Zoschke Reimo. . Structure of the actively translating plant 80S ribosome at 2.2 Å resolution Nature Plants
8ifc Feb. 17, 2023 Tomono Junta, Asano Kosuke, Chiashi Takuma, Suzuki Masato, Igarashi Masayuki, Takahashi Yoshiaki, Tanaka Yoshikazu, Yokoyama Takeshi. . Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside The Journal of Biochemistry
4fau May 22, 2012 Marcia Marco, Pyle Anna Marie. . Visualizing Group II Intron Catalysis through the Stages of Splicing Cell
8eiu Sept. 15, 2022 Nissley Amos J, Penev Petar I, Watson Zoe L, Banfield Jillian F, Cate Jamie H D. . Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome Nucleic Acids Research
4r0d July 30, 2014 Robart Aaron R., Chan Russell T., Peters Jessica K., Rajashankar Kanagalaghatta R., Toor Navtej. . Crystal structure of a eukaryotic group II intron lariat Nature
8am9 Aug. 3, 2022 Koller Timm O., Morici Martino, Berger Max, Safdari Haaris A., Lele Deepti S., Beckert Bertrand, Kaur Kanwal J., Wilson Daniel N.. . Structural basis for translation inhibition by the glycosylated drosocin peptide Nature Chemical Biology
1xpf Oct. 8, 2004 Ennifar Eric, Dumas Philippe. . Polymorphism of Bulged-out Residues in HIV-1 RNA DIS Kissing Complex and Structure Comparison with Solution Studies Journal of Molecular Biology
8btk Nov. 29, 2022 Jaskolowski Mateusz, Jomaa Ahmad, Gamerdinger Martin, Shrestha Sandeep, Leibundgut Marc, Deuerling Elke, Ban Nenad. . Molecular basis of the TRAP complex function in ER protein biogenesis Nature Structural & Molecular Biology
4e8m March 20, 2012 Marcia Marco, Pyle Anna Marie. . Visualizing Group II Intron Catalysis through the Stages of Splicing Cell
6chr Feb. 22, 2018 Chan Russell T., Peters Jessica K., Robart Aaron R., Wiryaman Timothy, Rajashankar Kanagalaghatta R., Toor Navtej. . Structural basis for the second step of group II intron splicing Nature Communications
8b2l Sept. 14, 2022 Smirnova Julia, Loerke Justus, Kleinau Gunnar, Schmidt Andrea, Bürger Jörg, Meyer Etienne H., Mielke Thorsten, Scheerer Patrick, Bock Ralph, Spahn Christian M. T., Zoschke Reimo. . Structure of the actively translating plant 80S ribosome at 2.2 Å resolution Nature Plants
4nfo Oct. 31, 2013 Phelps Kelly J., Ibarra-Soza José M., Tran Kiet, Fisher Andrew J., Beal Peter A.. . Click Modification of RNA at Adenosine: Structure and Reactivity of 7-Ethynyl- and 7-Triazolyl-8-aza-7-deazaadenosine in RNA ACS Chemical Biology
6gaw April 13, 2018 Kummer Eva, Leibundgut Marc, Rackham Oliver, Lee Richard G., Boehringer Daniel, Filipovska Aleksandra, Ban Nenad. . Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM Nature
1n7a Nov. 13, 2002 Ravelli Raimond B.G., Leiros Hanna-Kirsti Schrøder, Pan Baocheng, Caffrey Martin, McSweeney Sean. . Specific Radiation Damage Can Be Used to Solve Macromolecular Crystal Structures Structure
6t3r Oct. 11, 2019 Manigrasso Jacopo, Chillón Isabel, Genna Vito, Vidossich Pietro, Somarowthu Srinivas, Pyle Anna Marie, De Vivo Marco, Marcia Marco. . Visualizing group II intron dynamics between the first and second steps of splicing Nature Communications
8p2k May 16, 2023 Gamerdinger Martin, Jia Min, Schloemer Renate, Rabl Laurenz, Jaskolowski Mateusz, Khakzar Katrin M., Ulusoy Zeynel, Wallisch Annalena, Jomaa Ahmad, Hunaeus Gundula, Scaiola Alain, Diederichs Kay, Ban Nenad, Deuerling Elke. . NAC controls cotranslational N-terminal methionine excision in eukaryotes Science
4faw May 22, 2012 Marcia Marco, Pyle Anna Marie. . Visualizing Group II Intron Catalysis through the Stages of Splicing Cell
6t3r Oct. 11, 2019 Manigrasso Jacopo, Chillón Isabel, Genna Vito, Vidossich Pietro, Somarowthu Srinivas, Pyle Anna Marie, De Vivo Marco, Marcia Marco. . Visualizing group II intron dynamics between the first and second steps of splicing Nature Communications
5vjb April 19, 2017 Reiss Caroline W., Strobel Scott A.. . Structural basis for ligand binding to the guanidine-II riboswitch RNA
1n7a Nov. 13, 2002 Ravelli Raimond B.G., Leiros Hanna-Kirsti Schrøder, Pan Baocheng, Caffrey Martin, McSweeney Sean. . Specific Radiation Damage Can Be Used to Solve Macromolecular Crystal Structures Structure
1fuf Sept. 15, 2000
5v1l March 2, 2017 Schlegel Mark K., Foster Donald J., Kel’in Alexander V., Zlatev Ivan, Bisbe Anna, Jayaraman Muthusamy, Lackey Jeremy G., Rajeev Kallanthottathil G., Charissé Klaus, Harp Joel, Pallan Pradeep S., Maier Martin A., Egli Martin, Manoharan Muthiah. . Chirality Dependent Potency Enhancement and Structural Impact of Glycol Nucleic Acid Modification on siRNA Journal of the American Chemical Society
4e8n March 20, 2012 Marcia Marco, Pyle Anna Marie. . Visualizing Group II Intron Catalysis through the Stages of Splicing Cell
8emm Sept. 28, 2022 Watson Zoe L., Knudson Isaac J., Ward Fred R., Miller Scott J., Cate Jamie H. D., Schepartz Alanna, Abramyan Ara M.. . Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates Nature Chemistry
6ydp March 20, 2020 Kummer Eva, Ban Nenad. . Structural insights into mammalian mitochondrial translation elongation catalyzed by mt EFG 1 The EMBO Journal
2tra Nov. 6, 1987 Westhof E., Dumas Ph., Moras D.. . Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals Acta Crystallographica Section A Foundations of Crystallography
6ydw March 21, 2020 Kummer Eva, Ban Nenad. . Structural insights into mammalian mitochondrial translation elongation catalyzed by mt EFG 1 The EMBO Journal
4fb0 May 22, 2012 Marcia Marco, Pyle Anna Marie. . Visualizing Group II Intron Catalysis through the Stages of Splicing Cell
4e8t March 20, 2012 Marcia Marco, Pyle Anna Marie. . Visualizing Group II Intron Catalysis through the Stages of Splicing Cell
6uej Sept. 21, 2019 Meagher Jennifer L., Takata Matthew, Gonçalves-Carneiro Daniel, Keane Sarah C., Rebendenne Antoine, Ong Heley, Orr Victoria K., MacDonald Margaret R., Stuckey Jeanne A., Bieniasz Paul D., Smith Janet L.. . Structure of the zinc-finger antiviral protein in complex with RNA reveals a mechanism for selective targeting of CG-rich viral sequences Proceedings of the National Academy of Sciences
1n7b Nov. 13, 2002 Ravelli Raimond B.G., Leiros Hanna-Kirsti Schrøder, Pan Baocheng, Caffrey Martin, McSweeney Sean. . Specific Radiation Damage Can Be Used to Solve Macromolecular Crystal Structures Structure
6t3k Oct. 11, 2019 Manigrasso Jacopo, Chillón Isabel, Genna Vito, Vidossich Pietro, Somarowthu Srinivas, Pyle Anna Marie, De Vivo Marco, Marcia Marco. . Visualizing group II intron dynamics between the first and second steps of splicing Nature Communications
1i2y Feb. 12, 2001 TERESHKO VALENTINA, WALLACE SCOT T., USMAN NASSIM, WINCOTT FRANCINE E., EGLI MARTIN. . X-ray crystallographic observation of “in-line” and “adjacent” conformations in a bulged self-cleaving RNA/DNA hybrid RNA
7nql March 1, 2021 Kummer Eva, Schubert Katharina Noel, Schoenhut Tanja, Scaiola Alain, Ban Nenad. . Structural basis of translation termination, rescue, and recycling in mammalian mitochondria Molecular Cell
8g6x Feb. 16, 2023 Majumdar Chandrima, Walker Joshua A., Francis Matthew B., Schepartz Alanna, Cate Jamie H. D.. . Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome ACS Central Science
4faq May 22, 2012 Marcia Marco, Pyle Anna Marie. . Visualizing Group II Intron Catalysis through the Stages of Splicing Cell
7oax April 20, 2021 Mieczkowski Mateusz, Steinmetzger Christian, Bessi Irene, Lenz Ann-Kathrin, Schmiedel Alexander, Holzapfel Marco, Lambert Christoph, Pena Vladimir, Höbartner Claudia. . Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine Nature Communications
4p5j March 17, 2014 Colussi Timothy M., Costantino David A., Hammond John A., Ruehle Grant M., Nix Jay C., Kieft Jeffrey S.. . The structural basis of transfer RNA mimicry and conformational plasticity by a viral RNA Nature
7l0z Dec. 13, 2020 Jeng Sunny C.Y., Trachman Robert J., Weissenboeck Florian, Truong Lynda, Link Katie A., Jepsen Mette D.E., Knutson Jay R., Andersen Ebbe S., Ferré-D'Amaré Adrian R., Unrau Peter J.. . Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET RNA
2o3y Dec. 2, 2006 Kondo Jiro, Hainrichson Mariana, Nudelman Igor, Shallom‐Shezifi Dalia, Barbieri Christopher M., Pilch Daniel S., Westhof Eric, Baasov Timor. . Differential Selectivity of Natural and Synthetic Aminoglycosides towards the Eukaryotic and Prokaryotic Decoding A Sites ChemBioChem
7qi5 Dec. 14, 2021 Singh Vivek, Itoh Yuzuru, Del’Olio Samuel, Hassan Asem, Naschberger Andreas, Flygaard Rasmus Kock, Nobe Yuko, Izumikawa Keiichi, Aibara Shintaro, Andréll Juni, Whitford Paul C, Barrientos Antoni, Taoka Masato, Amunts Alexey. . Structure of mitoribosome reveals mechanism of mRNA binding, tRNA interactions with L1 stalk, roles of cofactors and rRNA modifications []
1n7b Nov. 13, 2002 Ravelli Raimond B.G., Leiros Hanna-Kirsti Schrøder, Pan Baocheng, Caffrey Martin, McSweeney Sean. . Specific Radiation Damage Can Be Used to Solve Macromolecular Crystal Structures Structure
7qi6 Dec. 14, 2021 Singh Vivek, Itoh Yuzuru, Del’Olio Samuel, Hassan Asem, Naschberger Andreas, Flygaard Rasmus Kock, Nobe Yuko, Izumikawa Keiichi, Aibara Shintaro, Andréll Juni, Whitford Paul C, Barrientos Antoni, Taoka Masato, Amunts Alexey. . Structure of mitoribosome reveals mechanism of mRNA binding, tRNA interactions with L1 stalk, roles of cofactors and rRNA modifications []
5ob3 June 26, 2017 Fernandez-Millan Pablo, Autour Alexis, Ennifar Eric, Westhof Eric, Ryckelynck Michael. . Crystal structure and fluorescence properties of the iSpinach aptamer in complex with DFHBI RNA
1tn2 Aug. 22, 1986 Brown R. S., Dewan J. C., Klug A.. . Crystallographic and biochemical investigation of the lead(II)-catalyzed hydrolysis of yeast phenylalanine tRNA Biochemistry

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 202.22 g/mol
HBA 4
HBD 4
HBA + HBD
AlogP -0.36
TPSA 76.10
RB 11

Radar chart