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micronomicin   Click here for help

GtoPdb Ligand ID: 12162

Synonyms: gentamicin C2b | Sagamicin® | XK-62-2
Approved drug
micronomicin is an approved drug (Japan)
Compound class: Natural product
Comment: Micronomicin belongs to the aminoglycoside class of antibacterial compounds and was originally isolated from Micromonospora sagamiensis [2]. It is an analogue of gentamicin.

micronomicin is commercially available from our sponsors

2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 12
Hydrogen bond donors 8
Rotatable bonds 7
Topological polar surface area 199.73
Molecular weight 463.3
XLogP -3.34
No. Lipinski's rules broken 2

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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Canonical SMILES CNC[C@@H]1CC[C@H]([C@H](O1)O[C@@H]1[C@@H](N)C[C@H]([C@@H]([C@H]1O)O[C@H]1OC[C@]([C@@H]([C@H]1O)NC)(C)O)N)N
Isomeric SMILES C[C@@]1(CO[C@@H]([C@@H]([C@H]1NC)O)O[C@H]1[C@@H](C[C@@H]([C@H]([C@@H]1O)O[C@@H]1[C@@H](CC[C@H](O1)CNC)N)N)N)O
InChI InChI=1S/C20H41N5O7/c1-20(28)8-29-19(14(27)17(20)25-3)32-16-12(23)6-11(22)15(13(16)26)31-18-10(21)5-4-9(30-18)7-24-2/h9-19,24-28H,4-8,21-23H2,1-3H3/t9-,10+,11-,12+,13-,14+,15+,16-,17+,18+,19+,20-/m0/s1
InChI Key DNYGXMICFMACRA-XHEDQWPISA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
Classification Click here for help
Compound class Natural product
Approved drug? Yes. Japan PMDA (0)
IUPAC Name Click here for help
(2R,3R,4R,5R)-2-[(1S,2S,3R,4S,6R)-4,6-diamino-3-[(2R,3R,6S)-3-amino-6-(methylaminomethyl)oxan-2-yl]oxy-2-hydroxycyclohexyl]oxy-5-methyl-4-(methylamino)oxane-3,5-diol
International Nonproprietary Names Click here for help
INN number INN
5036 micronomicin
Synonyms Click here for help
gentamicin C2b | Sagamicin® | XK-62-2
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo Micronomicin
Other databases
CAS Registry No. 52093-21-7 (source: Scifinder)
ChEBI CHEBI:81283
ChEMBL Ligand CHEMBL373081
DrugBank Ligand DB13274
DrugCentral Ligand 1801
GtoPdb PubChem SID 472319284
PubChem CID 3037206
Search Google for chemical match using the InChIKey DNYGXMICFMACRA-XHEDQWPISA-N
Search Google for chemicals with the same backbone DNYGXMICFMACRA
Search PubMed clinical trials micronomicin
Search PubMed titles micronomicin
Search PubMed titles/abstracts micronomicin
UniChem Compound Search for chemical match using the InChIKey DNYGXMICFMACRA-XHEDQWPISA-N
UniChem Connectivity Search for chemical match using the InChIKey DNYGXMICFMACRA-XHEDQWPISA-N

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MedChemExpress
Micronomicin (links to external site)
Cat. No. HY-B1915