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ribostamycin   Click here for help

GtoPdb Ligand ID: 12161

Synonyms: SF-733
PDB Ligand
Compound class: Natural product
Comment: Ribostamycin belongs to the aminoglycoside class of antibacterial compounds and was originally isolated from Streptomyces ribosidificus [1].
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 14
Hydrogen bond donors 10
Rotatable bonds 6
Topological polar surface area 262.38
Molecular weight 454.23
XLogP -4.81
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 OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)O[C@H]1[C@H](O[C@H]2O[C@H](CN)[C@H]([C@@H]([C@H]2N)O)O)[C@@H](N)C[C@H]([C@@H]1O)N
Isomeric SMILES C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CN)O)O)N)O[C@H]1[C@@H]([C@@H]([C@H](O1)CO)O)O)O)N
InChI InChI=1S/C17H34N4O10/c18-2-6-10(24)12(26)8(21)16(28-6)30-14-5(20)1-4(19)9(23)15(14)31-17-13(27)11(25)7(3-22)29-17/h4-17,22-27H,1-3,18-21H2/t4-,5+,6-,7-,8-,9+,10-,11-,12-,13-,14-,15-,16-,17+/m1/s1
InChI Key NSKGQURZWSPSBC-VVPCINPTSA-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
IUPAC Name Click here for help
(2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-2-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-3-hydroxycyclohexyl]oxyoxane-3,4-diol
International Nonproprietary Names Click here for help
INN number INN
3197 ribostamycin
Synonyms Click here for help
SF-733
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo Ribostamycin
Other databases
CAS Registry No. 25546-65-0 (source: Scifinder)
ChEBI CHEBI:45257
ChEMBL Ligand CHEMBL221572
DrugBank Ligand DB03615
DrugCentral Ligand 3526
GtoPdb PubChem SID 472319283
PubChem CID 33042
RCSB PDB Ligand RIO, RIO
Search Google for chemical match using the InChIKey NSKGQURZWSPSBC-VVPCINPTSA-N
Search Google for chemicals with the same backbone NSKGQURZWSPSBC
Search PubMed clinical trials ribostamycin
Search PubMed titles ribostamycin
Search PubMed titles/abstracts ribostamycin
UniChem Compound Search for chemical match using the InChIKey NSKGQURZWSPSBC-VVPCINPTSA-N
UniChem Connectivity Search for chemical match using the InChIKey NSKGQURZWSPSBC-VVPCINPTSA-N