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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
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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 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
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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 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/)
Classification Click here for help
Compound class Natural product
IUPAC Name Click here for help
[(1S,3R,4R,5R,6R,7S,8R,11S,13S,16S,17R,18E)-6-hydroxy-16-[(1R)-1-hydroxyethyl]-13-methoxy-5,17,19-trimethyl-14-oxo-2,15-dioxatetracyclo[9.8.0.01,7.03,8]nonadeca-9,18-dien-4-yl] 1H-pyrrole-2-carboxylate
Synonyms Click here for help
CP 47,444
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo Nargenicin
Other databases
CAS Registry No. 70695-02-2 (source: Scifinder)
PubChem CID 6326334
RCSB PDB Ligand 82W
Search Google for chemical match using the InChIKey YEUSSARNQQYBKH-SIMZXIQRSA-N
Search Google for chemicals with the same backbone YEUSSARNQQYBKH
UniChem Compound Search for chemical match using the InChIKey YEUSSARNQQYBKH-SIMZXIQRSA-N
UniChem Connectivity Search for chemical match using the InChIKey YEUSSARNQQYBKH-SIMZXIQRSA-N