MiMeDB: Showing metabocard for Actinonin (MMDBc0007839)

Pharmaceutical

Xenobiotic

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 00:52:57 UTC

Update Date

2025-10-07 16:04:15 UTC

Metabolite ID

MMDBc0007839

Metabolite Identification

Common Name

Actinonin

Description

Actinonin is a hydroxamate-containing metabolite classified as a peptide deformylase (PDF) inhibitor. Its chemical structure features an N-hydroxy-2-pentyl-succinamyl (HPS) moiety, which is crucial for its metal chelation properties and contributes to its activity against metalloproteinases. Actinonin is recognized as the most potent natural inhibitor of PDF, a key enzyme involved in bacterial protein synthesis, thereby exerting significant antimicrobial and herbicidal effects (PMID:40388608 ). The compound has been studied through various methods, including molecular docking and molecular dynamics simulations, which demonstrated its stability within the binding pocket of PDF (PMID:40319818 ). Additionally, actinonin is involved in pathways related to mitophagy enhancement, as evidenced by studies using immortalized mouse hippocampal neurons (PMID:40157622 ). Structural analyses have revealed the binding interactions of actinonin with nickel(II) and zinc(II) in PDF from Legionella pneumophila, providing insights into its inhibitory mechanism (PMID:40091854 ). Overall, actinonin exemplifies a significant chemical entity with diverse applications in microbiology and potential therapeutic implications.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Not Available

Molecular Formula

C₁₉H₃₅N₃O₅

Average Mass

385.4983

Monoisotopic Mass

385.257671245

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

Not Available

InChI Identifier

InChI=1S/C19H35N3O5/c1-4-5-6-8-14(11-16(24)21-27)18(25)20-17(13(2)3)19(26)22-10-7-9-15(22)12-23/h13-15,17,23,27H,4-12H2,1-3H3,(H,20,25)(H,21,24)/t14-,15+,17+/m1/s1

InChI Key

XJLATMLVMSFZBN-VYDXJSESSA-N

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Not Available

Spectra

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-23	95.4
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	65.9
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	449.0
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	504.5
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	426.4
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-23	168.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	2312.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	254.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	290.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	350.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	173.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	151.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	171.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	13.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	233.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	142.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	349.9
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1365.6
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	982.6

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	Actinonin_TMS_1	CCCCC[C@H](CC(=O)NO)C(=O)N[C@H](C(=O)N1CCC[C@H]1CO[Si](C)(C)C)C(C)C	standard non polar	2025-10-23	1226.22
Gas Chromatography	Actinonin_TMS_2	CCCCC[C@H](CC(=O)N(O)[Si](C)(C)C)C(=O)N[C@H](C(=O)N1CCC[C@H]1CO)C(C)C	standard non polar	2025-10-23	1299.39
Gas Chromatography	Actinonin_TMS_3	CCCCC[C@H](CC(=O)NO)C(=O)N([C@H](C(=O)N1CCC[C@H]1CO)C(C)C)[Si](C)(C)C	standard non polar	2025-10-23	2234.34
Gas Chromatography	Actinonin_TMS_4	CCCCC[C@H](CC(=O)N(O)[Si](C)(C)C)C(=O)N[C@H](C(=O)N1CCC[C@H]1CO[Si](C)(C)C)C(C)C	standard non polar	2025-10-23	1992.99
Gas Chromatography	Actinonin_TMS_5	CCCCC[C@H](CC(=O)NO)C(=O)N([C@H](C(=O)N1CCC[C@H]1CO[Si](C)(C)C)C(C)C)[Si](C)(C)C	standard non polar	2025-10-23	1417.87
Gas Chromatography	Actinonin_TMS_6	CCCCC[C@H](CC(=O)N(O)[Si](C)(C)C)C(=O)N([C@H](C(=O)N1CCC[C@H]1CO)C(C)C)[Si](C)(C)C	standard non polar	2025-10-23	2281.27
Gas Chromatography	Actinonin_TMS_7	CCCCC[C@H](CC(=O)N(O)[Si](C)(C)C)C(=O)N([C@H](C(=O)N1CCC[C@H]1CO[Si](C)(C)C)C(C)C)[Si](C)(C)C	standard non polar	2025-10-23	880.141
Gas Chromatography	Actinonin_TMS_1	CCCCC[C@H](CC(=O)NO)C(=O)N[C@H](C(=O)N1CCC[C@H]1CO[Si](C)(C)C)C(C)C	standard polar	2025-10-23	1019.26
Gas Chromatography	Actinonin_TMS_2	CCCCC[C@H](CC(=O)N(O)[Si](C)(C)C)C(=O)N[C@H](C(=O)N1CCC[C@H]1CO)C(C)C	standard polar	2025-10-23	2178.3
Gas Chromatography	Actinonin_TMS_3	CCCCC[C@H](CC(=O)NO)C(=O)N([C@H](C(=O)N1CCC[C@H]1CO)C(C)C)[Si](C)(C)C	standard polar	2025-10-23	2133.87
Gas Chromatography	Actinonin_TMS_4	CCCCC[C@H](CC(=O)N(O)[Si](C)(C)C)C(=O)N[C@H](C(=O)N1CCC[C@H]1CO[Si](C)(C)C)C(C)C	standard polar	2025-10-23	1982.67
Gas Chromatography	Actinonin_TMS_5	CCCCC[C@H](CC(=O)NO)C(=O)N([C@H](C(=O)N1CCC[C@H]1CO[Si](C)(C)C)C(C)C)[Si](C)(C)C	standard polar	2025-10-23	2759.68
Gas Chromatography	Actinonin_TMS_6	CCCCC[C@H](CC(=O)N(O)[Si](C)(C)C)C(=O)N([C@H](C(=O)N1CCC[C@H]1CO)C(C)C)[Si](C)(C)C	standard polar	2025-10-23	2158.67
Gas Chromatography	Actinonin_TMS_7	CCCCC[C@H](CC(=O)N(O)[Si](C)(C)C)C(=O)N([C@H](C(=O)N1CCC[C@H]1CO[Si](C)(C)C)C(C)C)[Si](C)(C)C	standard polar	2025-10-23	1973.54

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Actinobacteria	1	Human	Metabolic reconstruction
Bacteria	Actinobacteria	1	Human	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Drugs - Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Blood	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	31557052

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Actinonin (MMDBc0007839)

MOL for #<Metabolite:0x00007f2e28cdade0>

3D MOL for #<Metabolite:0x00007f2e28cdade0>

3D SDF for #<Metabolite:0x00007f2e28cdade0>

3D-SDF for #<Metabolite:0x00007f2e28cdade0>

PDB for #<Metabolite:0x00007f2e28cdade0>

3D PDB for #<Metabolite:0x00007f2e28cdade0>

SMILES for #<Metabolite:0x00007f2e28cdade0>

INCHI for #<Metabolite:0x00007f2e28cdade0>

Structure for #<Metabolite:0x00007f2e28cdade0>

3D Structure for #<Metabolite:0x00007f2e28cdade0>