apramycin   Click here for help

GtoPdb Ligand ID: 10760

Synonyms: EBL-1003 | EL-857 | EL857 | nebramycin factor 2 | nebramycin II
PDB Ligand
Compound class: Natural product
Comment: Apramycin is an aminoglycoside antibacterial compound that was originally isolated from Streptomyces tenebrarius. The compound has activity against Gram-negative bacteria [2,4].
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 16
Hydrogen bond donors 11
Rotatable bonds 6
Topological polar surface area 283.64
Molecular weight 539.28
XLogP -4.99
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 CN[C@@H]1[C@H](O[C@@H]2[C@@H]([C@@H]1O)O[C@@H]([C@@H](C2)N)O[C@@H]1[C@@H](N)C[C@H]([C@@H]([C@H]1O)O)N)O[C@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)N
Isomeric SMILES CN[C@@H]1[C@H](O[C@@H]2[C@@H]([C@@H]1O)O[C@@H]([C@@H](C2)N)O[C@@H]1[C@@H](N)C[C@H]([C@@H]([C@H]1O)O)N)O[C@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)N
InChI InChI=1S/C21H41N5O11/c1-26-11-14(30)18-8(33-20(11)37-21-16(32)13(29)10(25)9(4-27)34-21)3-7(24)19(36-18)35-17-6(23)2-5(22)12(28)15(17)31/h5-21,26-32H,2-4,22-25H2,1H3/t5-,6+,7-,8+,9-,10-,11+,12+,13+,14-,15-,16-,17-,18+,19+,20-,21-/m1/s1
InChI Key XZNUGFQTQHRASN-XQENGBIVSA-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/)
References
1. Almabruk KH, Chang JH, Mahmud T. (2016)
Total Synthesis of (±)-Isoperbergins and Correction of the Chemical Structure of Perbergin.
J Nat Prod, 79 (9): 2391-6. [PMID:27588436]
2. Kang AD, Smith KP, Eliopoulos GM, Berg AH, McCoy C, Kirby JE. (2017)
Invitro Apramycin Activity against multidrug-resistant Acinetobacter baumannii and Pseudomonas aeruginosa.
Diagn Microbiol Infect Dis, 88 (2): 188-191. [PMID:28341099]
3. Roch M, Sierra R, Sands K, Martins WMBS, Schrenzel J, Walsh TR, Gales AC, Andrey DO. (2021)
Vertical and horizontal dissemination of an IncC plasmid harbouring rmtB 16S rRNA methylase gene, conferring resistance to plazomicin, among invasive ST258 and ST16 KPC-producing Klebsiella pneumoniae.
J Glob Antimicrob Resist, 24: 183-189. [PMID:33373732]
4. Sheng Y, Lam PW, Shahab S, Santosa DA, Proteau PJ, Zabriskie TM, Mahmud T. (2015)
Identification of Elaiophylin Skeletal Variants from the Indonesian Streptomyces sp. ICBB 9297.
J Nat Prod, 78 (11): 2768-75. [PMID:26510047]
5.  Juvabis Announces Positive Phase 1 Results of EBL-1003 in the Innovative Medicines Initiative’s ENABLE Consortium.
Accessed on 23/02/2023. Modified on 23/02/2023. AMR Conference, https://amr-conference.com/news/juvabis-announces-positive-phase-1-results-of-ebl-1003-in-the-innovative-medicines-initiatives-enable-consortium/