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

nargenicin A1   Click here for help

GtoPdb Ligand ID: 14528

Synonyms: CP 47,444
PDB Ligand
Compound class: Natural product
Comment: Nargenicin A1 is a macrolide antibacterial, first isolated from the soil-dwelling actinomycete Nocardia argentinensis [1]. It has narrow-spectrum Gram-positive antibacterial activity (principally anti-Staphylococcus activity), inhibiting bacterial DNA replication by targeting DNA polymerase III subunit alpha (DnaE) [3]. A more recent study has found that Nargenicin A1 has antimycobacterial activity and is an inhibitor of Mycobacterium tuberculosis DnaE1 [2].
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 9
Hydrogen bond donors 3
Rotatable bonds 5
Topological polar surface area 123.55
Molecular weight 515.6
XLogP 1.14
No. Lipinski's rules broken 1

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 C[C@@H]1/C=C(\C)/[C@@]23[C@]([H])(C=C[C@]4([H])[C@@]3([H])[C@@H]([C@@H](C)[C@H]([C@@H]4O2)OC(=O)C5=CC=CN5)O)C[C@@H](C(=O)O[C@]1([H])[C@@H](C)O)OC
Isomeric SMILES C/C=1/[C@@]23O[C@H]4[C@@H]([C@@H]([C@H]([C@]2([H])[C@@]4([H])C=C[C@]3([H])C[C@H](OC)C(O[C@]([C@@H](/C1)C)([H])[C@H](O)C)=O)O)C)OC(C5=CC=CN5)=O
InChI InChI=1S/C28H37NO8/c1-13-11-14(2)28-17(12-20(34-5)27(33)35-23(13)16(4)30)8-9-18-21(28)22(31)15(3)24(25(18)37-28)36-26(32)19-7-6-10-29-19/h6-11,13,15-18,20-25,29-31H,12H2,1-5H3/b14-11+/t13-,15-,16-,17-,18-,20+,21+,22-,23+,24-,25-,28+/m1/s1
InChI Key YEUSSARNQQYBKH-SIMZXIQRSA-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/)
Bioactivity Comments
The MIC for antimycobacterial activity in vitro is 12.5 μM against M. tuberculosis H37Rv [2].