HARIBOSS

Harnessing RIBOnucleic acid - Small molecules Structures

Compound SFG

Identifiers

  • Canonical SMILES: 
    N[C@@H](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  • IUPAC name: 
    (2S,5S)-2,5-diamino-6-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]hexanoic acid (non-preferred name)
  • InChi: 
    InChI=1S/C15H23N7O5/c16-6(1-2-7(17)15(25)26)3-8-10(23)11(24)14(27-8)22-5-21-9-12(18)19-4-20-13(9)22/h4-8,10-11,14,23-24H,1-3,16-17H2,(H,25,26)(H2,18,19,20)/t6-,7-,8+,10+,11+,14+/m0/s1
  • InChiKey: 
    LMXOHSDXUQEUSF-YECHIGJVSA-N

Chemistry rules

Lipinski's RO5 Veber Pfizer's 3/75

External links

65482 CHEMBL1214186 DB01910

RNA-SM complexes

PDB code Deposition date Reference publication
3gx2 April 1, 2009 Montange Rebecca K., Mondragón Estefanía, van Tyne Daria, Garst Andrew D., Ceres Pablo, Batey Robert T.. . Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch Journal of Molecular Biology
4ox9 Feb. 4, 2014 Dunkle Jack A., Vinal Kellie, Desai Pooja M., Zelinskaya Natalia, Savic Miloje, West Dayne M., Conn Graeme L., Dunham Christine M.. . Molecular recognition and modification of the 30S ribosome by the aminoglycoside-resistance methyltransferase NpmA Proceedings of the National Academy of Sciences
5wwr Jan. 4, 2017 Liu Ru-Juan, Long Tao, Li Jing, Li Hao, Wang En-Duo. . Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6 Nucleic Acids Research
5wwr Jan. 4, 2017 Liu Ru-Juan, Long Tao, Li Jing, Li Hao, Wang En-Duo. . Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6 Nucleic Acids Research
9imb July 2, 2024 Zhong Fumei, Pu Tian, Hu Qian, Li Mingwei, Wang Lei, Wang Suman, Ruan Ke, Shi Yunyu, Sun Beicheng, Jiang Yiyang, Lv Mengqi. . NSUN6 inhibitor discovery guided by its mRNA substrate bound crystal structure Structure
9imb July 2, 2024 Zhong Fumei, Pu Tian, Hu Qian, Li Mingwei, Wang Lei, Wang Suman, Ruan Ke, Shi Yunyu, Sun Beicheng, Jiang Yiyang, Lv Mengqi. . NSUN6 inhibitor discovery guided by its mRNA substrate bound crystal structure Structure
9j5p Aug. 13, 2024 Yoo J, Lee Y, Cho G, Lim J, Kim J. . Pending: 10.1093/nar/gkaf751 None
9z2r Nov. 5, 2025 Canepa Jacob, Ruiz-Arroyo Victor M., Schlamowitz Netanya S., Nam Yunsun. . Substrate selectivity of the human RNA m5C methyltransferase NSUN2 Nature
9z2t Nov. 5, 2025 Canepa Jacob, Ruiz-Arroyo Victor M., Schlamowitz Netanya S., Nam Yunsun. . Substrate selectivity of the human RNA m5C methyltransferase NSUN2 Nature

Physicochemical filters

Descriptor Lipinski's RO5 Veber Pfizer's 3/75
Compliance
MW 381.18 g/mol
HBA 10
HBD 6
HBA + HBD
AlogP -2.06
TPSA 208.65
RB 7

Radar chart