Hygromycin B - ≥60%(HPLC), Powder , CAS No.31282-04-9

CAS: 31282-04-9 Cat. No.: H113147 Molecular Weight: 527.52 EC Number: 250-545-5

GRADE & PURITY ≥60%(HPLC), Powder

Synonyms

SMP1_000163 | BCBcMAP01_000235 | O-6-Amino-6-deoxy-L-glycero-D-galacto-heptopyranosylidene-(1-2-3)-O-beta-D-talopyranosyl(1-5)-2-deoxy-N3-methyl-D-streptamine | Hygromycin B, from Streptomyces hygroscopicus | GS-5543 | (2S,3R,3A'S,4S,4'S,5R,6R,6'R,7'S,7a'

Storage

Store at 2-8°C

Shipped In

Wet ice

Overview

An antibiotic often used for selection of cells transfected with E. coli hygromycin resistance gene.

Application：

An aminoglycoside antibiotic that kills bacteria by inhibiting protein synthesisHygromycin B is used for the selection and maintenance of prokaryotic and eukaryotic cells that contains the hygromycin resistance gene. This gene is frequently used as a selectable marker in research on plants. It stabilizes the transfer ribonucleic acid (tRNA)-ribosomal acceptor site, thereby inhibiting translocation. In addition to this, it serves as an aminoglycosidic antibiotic which inhibits protein synthesis.

Specifications

Synonyms

SMP1_000163 | BCBcMAP01_000235 | O-6-Amino-6-deoxy-L-glycero-D-galacto-heptopyranosylidene-(1-2-3)-O-beta-D-talopyranosyl(1-5)-2-deoxy-N3-methyl-D-streptamine | Hygromycin B, from Streptomyces hygroscopicus | GS-5543 | (2S, 3R, 3A'S, 4S, 4'S, 5R, 6R, 6'R, 7'S, 7a'

Specifications & Purity

≥60%(HPLC), Powder

Biochemical and Physiological Mechanisms

Aminoglycoside antibiotic. Active against both prokaryotic and eukaryotic cells. Inhibits protein synthesis by binding to the 30S subunit and inhibiting the ribosomal translocation step of elongation.

Storage

Store at 2-8°C

Shipped In

Wet ice

This product requires cold chain shipping. Ground and other economy services are not available.

Purity

≥60%(HPLC)

Names and Identifiers

• Canonical Smiles: CNC1CC(C(C(C1O)OC2C3C(C(C(O2)CO)O)OC4(O3)C(C(C(C(O4)C(CO)N)O)O)O)O)N
• IUPAC Name: (2S,3'R,3aS,4S,4'S,5'R,6R,6'R,7S,7aS)-4-[(1R,2S,3R,5S,6R)-3-amino-2,6-dihydroxy-5-(methylamino)cyclohexyl]oxy-6'-[(1R)-1-amino-2-hydroxyethyl]-6-(hydroxymethyl)spiro[4,6,7,7a-tetrahydro-3aH-[1,3]dioxolo[4,5-c]pyran-2,2'-oxane]-3',4',5',7-tetrol
• InChIKey: GRRNUXAQVGOGFE-XKIAHZFYSA-N
• INCHI: 1S/C20H37N3O13/c1-23-7-2-5(21)9(26)15(10(7)27)33-19-17-16(11(28)8(4-25)32-19)35-20(36-17)18(31)13(30)12(29)14(34-20)6(22)3-24/h5-19,23-31H,2-4,21-22H2,1H3/t5-,6-,7+,8-,9+,10-,11+,12-,13+,14-,15-,16+,17+,18-,19+,20+/m1/s1
• Isomeric SMILES: CN[C@H]1C[C@H]([C@@H]([C@H]([C@@H]1O)O[C@H]2[C@@H]3[C@H]([C@H]([C@H](O2)CO)O)O[C@]4(O3)[C@@H]([C@H]([C@H]([C@H](O4)[C@@H](CO)N)O)O)O)O)N
• UN Number: 3462
• Packing Group: I
• Molecular Weight: 527.52
• Reaxy-Rn: 1335986
• Reaxys-RN_link_address: https://www.reaxys.com/reaxys/secured/hopinto.do?context=S&query=IDE.XRN=1335986&ln=

Taxonomic Classification

Taxonomy Tree

• Kingdom Organic compounds
  • Superclass Organic oxygen compounds
    • Class Organooxygen compounds
      • Subclass Carbohydrates and carbohydrate conjugates
        • Level5 Aminosaccharides
          • Level6 Aminoglycosides
            • Level7 Aminocyclitol glycosides
              • Level8 2-deoxystreptamine aminoglycosides

• Kingdom: Organic compounds
• Superclass: Organic oxygen compounds
• Class: Organooxygen compounds
• Subclass: Carbohydrates and carbohydrate conjugates
• Intermediate Tree Nodes: Aminosaccharides - Aminoglycosides - Aminocyclitol glycosides
• Direct Parent: 2-deoxystreptamine aminoglycosides
• Alternative Parents: O-glycosyl compounds Disaccharides Dioxolopyrans Aminocyclitols and derivatives Ortho esters Cyclohexylamines Cyclohexanols Carboxylic acid orthoesters Oxanes 1,3-dioxolanes 1,2-aminoalcohols Polyols Oxacyclic compounds Dialkylamines Acetals Primary alcohols Organopnictogen compounds Monoalkylamines Hydrocarbon derivatives
• Molecular Framework: Aliphatic heteropolycyclic compounds
• Substituents: 2-deoxystreptamine aminoglycoside - O-glycosyl compound - Glycosyl compound - Disaccharide - Dioxolopyran - Aminocyclitol or derivatives - Ortho ester - Cyclohexylamine - Cyclohexanol - Carboxylic acid orthoester - Oxane - Cyclitol or derivatives - Cyclic alcohol - Meta-dioxolane - Secondary alcohol - Orthocarboxylic acid derivative - 1,2-aminoalcohol - Oxacycle - Organoheterocyclic compound - Secondary amine - Polyol - Secondary aliphatic amine - Acetal - Organic nitrogen compound - Organopnictogen compound - Hydrocarbon derivative - Primary amine - Primary alcohol - Organonitrogen compound - Primary aliphatic amine - Amine - Alcohol - Aliphatic heteropolycyclic compound
• Description: This compound belongs to the class of organic compounds known as 2-deoxystreptamine aminoglycosides. These are aminoglycosides containing the 2-deoxystreptamine (1,3-diaminocyclohexane-4,5,6-triol) core.
• External Descriptors: Not available

Data sources

1. Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61.

DOI: 10.1186/s13321-016-0174-y

Associated Targets(non-human)

Saccharomyces cerevisiae (19171 Activities)

Explore this target

Activity Type	Relation	Activity value	Units	Action Type	Journal	PubMed Id	doi	Assay Aladdin ID

Ustilago maydis (75 Activities)

Explore this target

Activity Type	Relation	Activity value	Units	Action Type	Journal	PubMed Id	doi	Assay Aladdin ID

Mechanisms of Action

Chemical and Physical Properties

• Solubility: Miscible with water, methanol, buffer solution and ethanol. Immiscible with less polar solvents.
• Sensitivity: Heat Sensitive
• Specific Rotation[α]: 20° (C=1,H2O)
• Melt Point(°C): 160-180°C
• Molecular Weight: 527.500 g/mol
• XLogP3: -6.600
• Hydrogen Bond Donor Count: 11
• Hydrogen Bond Acceptor Count: 16
• Rotatable Bond Count: 6
• Exact Mass: 527.233 Da
• Monoisotopic Mass: 527.233 Da
• Topological Polar Surface Area: 272.000 Ų
• Heavy Atom Count: 36
• Formal Charge: 0
• Complexity: 756.000
• Isotope Atom Count: 0
• Defined Atom Stereocenter Count: 16
• Undefined Atom Stereocenter Count: 0
• Defined Bond Stereocenter Count: 0
• Undefined Bond Stereocenter Count: 0
• The total count of all stereochemical bonds: 0
• Covalently-Bonded Unit Count: 1

References

1. Hao Zhou, Jiangbo Huang, Fang Wang.  (2023)  Increased transcription of hsa_circ_0000644 upon RUNX family transcription factor 3 downregulation participates in the malignant development of bladder cancer.  CELLULAR SIGNALLING,      [PMID:36627006] [10.1016/j.cellsig.2023.110590]

2. Yong Sun, Tingting Guo, Dawei Guo, Li Guo, Li Chen, Yu Zhang, Liping Wang.  (2016)  Establishment and characterization of an MDCK cell line stably-transfected with chicken Abcb1 encoding P-glycoprotein.  RESEARCH IN VETERINARY SCIENCE,      [PMID:27234533] [10.1016/j.rvsc.2016.03.004]

3. Wang Zhengwei, Lin Jiani, Tan Guisen, Pan Tingzheng, Zhang Hongtian, Liu Jiangang.  (2025)  miR-1270 suppresses glioblastoma development by transcriptional inhibition of nuclear factor IX.  MOLECULAR BIOLOGY REPORTS,  52  (1): (1-10).  [PMID:40815328] [10.1007/s11033-025-10915-3]

4. Daoyan Tang, Minggui Wang, Dan Wang, Danni Yang, Yi Cai, Tao Luo, Jianqing He, Qinglan Wang.  (2025)  Ultra-high field strength electroporation enables efficient DNA transformation and genome editing in nontuberculous mycobacteria.  Microbiology Spectrum,  13  (10):   [PMID:40920009] [10.1128/spectrum.01944-25]

5. Mengjun Yun, Yu Xiong, Zhuobing Wang, Lianjie Xie, Hanwen Ye, Xiaofang Yuan, Weiyi He, Binqing Chen, Zhanjun Lu, Wei Chen.  (2025)  Insect Oral Secretion Protein and Its Related Core Peptide Induce the Host Plant’s Endogenous Abscisic Acid to Enhance Resistance against Insect.  JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY,      [PMID:40270364] [10.1021/acs.jafc.4c12912]

6. Haobo Xing, Qingming Hou, Zhenhua Wang, Shanfei Zhang, Shangxia Song, Lulu Du, Chenghua Gao, Yunfei Li, Fubao Sun.  (2026)  Enhanced Monensin Biosynthesis in Streptomyces cinnamonensis with Multigene Integration and Overexpression of Newly Identified Genes.  BIOCHEMICAL ENGINEERING JOURNAL,      [PMID:] [10.1016/j.bej.2026.110118]