GtoPdb is requesting financial support from commercial users. Please see our sustainability page for more information.

vertilmicin   Click here for help

GtoPdb Ligand ID: 11018

Compound class: Synthetic organic
Comment: Vertilmicin is a semisynthetic aminoglycoside antibacterial that inhibits bacterial growth by inhibiting protein synthesis. It has Gram-negative and Gram-positive activity [1].
2D Structure
Click here for help

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.

✖
Click here for structure editor
Physico-chemical Properties
Click here for help

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.

✖
Hydrogen bond acceptors 12
Hydrogen bond donors 8
Rotatable bonds 8
Topological polar surface area 199.73
Molecular weight 489.32
XLogP -2.29
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
Click here for help

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/)

✖
Canonical SMILES CCN[C@@H]1C[C@H](N)[C@H]([C@@H]([C@H]1O[C@H]1OC[C@]([C@@H]([C@H]1O)NC)(C)O)O)O[C@H]1OC(=CC[C@H]1N)C(N)C
Isomeric SMILES CCN[C@@H]1C[C@H](N)[C@H]([C@@H]([C@H]1O[C@H]1OC[C@]([C@@H]([C@H]1O)NC)(C)O)O)O[C@H]1OC(=CC[C@H]1N)C(N)C
InChI InChI=1S/C22H43N5O7/c1-5-27-13-8-12(25)17(33-20-11(24)6-7-14(32-20)10(2)23)15(28)18(13)34-21-16(29)19(26-4)22(3,30)9-31-21/h7,10-13,15-21,26-30H,5-6,8-9,23-25H2,1-4H3/t10?,11-,12+,13-,15+,16-,17-,18+,19-,20-,21-,22+/m1/s1
InChI Key QVRLHIRFLRXFIW-OFMFRWEUSA-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 Synthetic organic
IUPAC Name Click here for help
(2R,3R,4R,5R)-2-[(1S,2S,3R,4S,6R)-4-amino-3-[[(2S,3R)-3-amino-6-(1-aminoethyl)-3,4-dihydro-2H-pyran-2-yl]oxy]-6-(ethylamino)-2-hydroxycyclohexyl]oxy-5-methyl-4-(methylamino)oxane-3,5-diol
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo Vertilmicin
Other databases
CAS Registry No. 59711-97-6 (source: PubChem)
GtoPdb PubChem SID 405560459
PubChem CID 101268397
Search Google for chemical match using the InChIKey QVRLHIRFLRXFIW-OFMFRWEUSA-N
Search Google for chemicals with the same backbone QVRLHIRFLRXFIW
UniChem Compound Search for chemical match using the InChIKey QVRLHIRFLRXFIW-OFMFRWEUSA-N
UniChem Connectivity Search for chemical match using the InChIKey QVRLHIRFLRXFIW-OFMFRWEUSA-N