SCS-C000114
lynamicin D
Pathway: Alkaloids
Superclass: Tryptophan alkaloids
Class: Simple indole alkaloids
Chemical Structure
Loading 3D structure...
3D conformers are computationally generated from SMILES by RDKit for visualization and download; they are not experimental crystal or NMR structures.
Source Information
Streptomyces marincola
(marine actinomycete)
Kingdom
Bacillati
Phylum
Actinomycetota
Class
Actinomycetes
Order
Kitasatosporales
Family
Streptomycetaceae
Genus
Streptomyces
Species
Streptomyces marincola
Luhuitou Peninsula
· 2m
· 18.50°N, 109.46°E
DOI:
10.3389/fmicb.2022.860308
· Frontiers in Microbiology
Streptomyces sp. SCSIO 11791
(bacterium)
Kingdom
Bacillati
Phylum
Actinomycetota
Class
Actinomycetes
Order
Kitasatosporales
Family
Streptomycetaceae
Genus
Streptomyces
Species
NA
South China Sea
· 1,765 m
DOI:
10.1038/s41429-020-0307-4
· The Journal of Antibiotics
Drug-likeness (Lipinski Ro5)
Molecular Weight
482.3 Da
Threshold ≤ 500
ALogP
6.19
Threshold ≤ 5
H-Bond Donors
3
Threshold ≤ 5
H-Bond Acceptors
4
Threshold ≤ 10
1 violation (ALogP) — borderline drug-like
Chemical Properties
Molecular Formula:
C24H17Cl2N3O4
Molecular Weight:
482.3000 Da
SMILES:
COC(=O)c1[nH]c(C(=O)OC)c(-c2c[nH]c3ccc(Cl)cc23)c1-c1c[nH]c2ccc(Cl)cc12
InChIKey:
YYBKJQDTRQASSS-UHFFFAOYSA-N
InChI:
InChI=1S/C24H17Cl2N3O4/c1-32-23(30)21-19(15-9-27-17-5-3-11(25)7-13(15)17)20(22(29-21)24(31)33-2)16-10-28-18-6-4-12(26)8-14(16)18/h3-10,27-29H,1-2H3
Calculated Properties
ALogP:
6.191 lipophilicity
TPSA:
99.97 Ų polar surface area
H-Bond Donors:
3
H-Bond Acceptors:
4
Rotatable Bonds:
4
Ring Count:
5
(5 aromatic)
Chiral Centers:
0
Fsp³:
0.0833 fraction sp³ carbon
Database Information
Compound ID:
SCS-C000114
NPClassifier Pathway:
Alkaloids
NPClassifier Superclass:
Tryptophan alkaloids
NPClassifier Class:
Simple indole alkaloids
Glycoside:
No
NPClassifier Status:
Classified
External Links:
General chemistry
Natural product databases
Biological Activity Data
Activity values are displayed only when a quantitative or clearly reported result is available.
Tested organisms, cell lines and molecular targets are shown under Target / model.
| Activity | Assay | Target / model | Result | Reference |
|---|---|---|---|---|
| Antitumor | — | cancer cell lines | cytotoxic | 10.3389/fmicb.2022.860308 Frontiers in Microbiology |
| Antitumor | IC50 | MDA-MB-435 human breast cancer cells | > 50.0 μM | 10.1038/s41429-020-0307-4 The Journal of Antibiotics |
| Antibacterial | MIC | Micrococcus luteus ML01, Staphylococcus aureus ATCC 29213 | 0.2–4.0 μg/mL | 10.1038/s41429-020-0307-4 The Journal of Antibiotics |
| Antibacterial | MIC | MRSA strains | 1.0–16.0 μg/mL | 10.1038/s41429-020-0307-4 The Journal of Antibiotics |