alchivemycin A   Click here for help

GtoPdb Ligand ID: 13437

Compound class: Natural product
Comment: Alchivemycin A is a polycyclic polyketide that was isolated from a plant-associated actinomycete Streptomyces species [2]. Spectroscopic analysis and X-ray crystallography were used to define its structure and absolute stereo configuration. We drew the structure as depicted in [2], and the resulting SMILES mapped to the PubChem CID listed below. Alchivemycin A has antimicrobial and anticancer properties in vitro [2-5]. A complex total synthesis that integrated traditional chemical methods and biocatalysis using enzymes engineered from the source bacterium, has been reported [1].
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 5
Rotatable bonds 3
Topological polar surface area 172.82
Molecular weight 647.8
XLogP 3.26
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=C(\C)/[C@@H]([C@@H]([C@H]1[C@H]([C@@H]([C@@H](C)CCCC[C@H]2[C@@](C)([C@]3([H])[C@H]([C@]4([H])[C@H](C)C[C@H](C)C[C@]4([H])[C@@H]5[C@H]3O5)C(=O)C6=C(CN1OC6=O)O)O2)O)O)O)O
Isomeric SMILES [H][C@]12C[C@@H](C)C[C@@H](C)[C@@]1([H])[C@@H]3C(=O)C4=C(O)CN(OC4=O)[C@@H]([C@@H](O)[C@@H](O)\C(\C)=C\C)[C@@H](O)[C@H](O)[C@@H](C)CCCC[C@@H]5O[C@]5(C)[C@@]3([H])[C@@H]6O[C@H]26
InChI InChI=1S/C35H53NO10/c1-7-16(3)27(38)30(41)26-31(42)28(39)17(4)10-8-9-11-21-35(6,45-21)25-24(29(40)23-20(37)14-36(26)46-34(23)43)22-18(5)12-15(2)13-19(22)32-33(25)44-32/h7,15,17-19,21-22,24-28,30-33,37-39,41-42H,8-14H2,1-6H3/b16-7+/t15-,17-,18+,19-,21-,22+,24-,25+,26-,27-,28+,30+,31+,32+,33-,35-/m0/s1
InChI Key ZEXKBCGEARGIOX-IGRLKBMTSA-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. Dong H, Guo N, Hu D, Hong B, Liao D, Zhu HJ, Yan ZY, Ge HM, Lei X. (2024)
Chemoenzymatic total synthesis of alchivemycin A.
Nat Synth,. DOI: 10.1038/s44160-024-00577-7
2. Igarashi Y, Kim Y, In Y, Ishida T, Kan Y, Fujita T, Iwashita T, Tabata H, Onaka H, Furumai T. (2010)
Alchivemycin A, a bioactive polycyclic polyketide with an unprecedented skeleton from Streptomyces sp.
Org Lett, 12 (15): 3402-5. [PMID:20670006]
3. Kim Y, In Y, Ishida T, Onaka H, Igarashi Y. (2013)
Biosynthetic origin of alchivemycin A, a new polyketide from Streptomyces and absolute configuration of alchivemycin B.
Org Lett, 15 (14): 3514-7. [PMID:23819828]
4. Onaka H, Mori Y, Igarashi Y, Furumai T. (2011)
Mycolic acid-containing bacteria induce natural-product biosynthesis in Streptomyces species.
Appl Environ Microbiol, 77 (2): 400-6. [PMID:21097597]
5. Zhu HJ, Zhang B, Wei W, Liu SH, Xiang L, Zhu J, Jiao RH, Igarashi Y, Bashiri G, Liang Y et al.. (2022)
AvmM catalyses macrocyclization through dehydration/Michael-type addition in alchivemycin A biosynthesis.
Nat Commun, 13 (1): 4499. [PMID:35922406]