MiMeDB: Showing metabocard for Serratin (MMDBc0003321)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-14 21:24:43 UTC

Update Date

2025-10-07 16:04:43 UTC

Metabolite ID

MMDBc0003321

Metabolite Identification

Common Name

Serratin

Description

Serratin is a bacterial metabolite belonging to the chemical class of oxazolidines, specifically derived from the bacterium Serratia marcescens. The compound has been characterized through various spectroscopic methods, including ultraviolet (UV) spectra, infrared (IR) spectra, electronic circular dichroism (ECD) spectra, mass spectrometry (MS), and nuclear magnetic resonance (NMR) (PMID:40619027 ). Biological studies have shown that serratin A, a derivative of serratin, induces apoptosis in MCF-7 cells, as evidenced by transcriptomic analyses revealing significant enrichment in apoptosis-related gene ontology (GO) and KEGG pathways (PMID:40619027 ). Annexin V/propidium iodide staining and mitochondrial membrane potential assays further confirmed that serratin A treatment leads to increased pro-apoptotic markers such as Bax and Caspase 3/9 while reducing the expression of the anti-apoptotic gene Bcl-2 in a dose-dependent manner (PMID:40619027 ). In vivo studies demonstrated that serratin A effectively inhibits tumor growth in MCF-7 tumor-bearing mice, correlating with increased apoptosis (PMID:40619027 ). Additionally, structural reassessment of serratin has led to the proposal of a symmetrical serratamolide analogue, correcting previous misassignments of its structure (PMID:28530397 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305142123242D          

 19 19  0  0  1  0            999 V2000
   -2.1969   -3.0012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4824   -3.4137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7680   -3.0012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0535   -3.4137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6610   -3.0012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3755   -3.4137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0283   -2.1785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6840   -2.3931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0899   -3.0012    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8613   -2.4548    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6330   -1.6173    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5599   -3.2227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4488   -1.7403    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0420   -1.6498    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3899   -0.8290    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1211   -3.8275    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7716   -3.4659    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0591   -3.8256    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3512   -3.1186    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  9  6  1  6  0  0  0
  9  7  1  0  0  0  0
 10  8  1  1  0  0  0
 11  7  1  0  0  0  0
 12 10  1  0  0  0  0
 13 10  1  0  0  0  0
 13 11  2  0  0  0  0
 14  8  1  0  0  0  0
 15 11  1  0  0  0  0
 16 12  2  0  0  0  0
 17  9  1  0  0  0  0
 17 12  1  0  0  0  0
  9 18  1  1  0  0  0
 10 19  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0003321

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(CCCCCC)CC(O)=N[C@@]([H])(CO)C(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C12H21NO4/c1-2-3-4-5-6-9-7-11(15)13-10(8-14)12(16)17-9/h9-10,14H,2-8H2,1H3,(H,13,15)/t9-,10+/m1/s1

> <INCHI_KEY>
STXCXCAUQNUQQP-ZJUUUORDSA-N

> <FORMULA>
C12H21NO4

> <MOLECULAR_WEIGHT>
243.303

> <EXACT_MASS>
243.14705816

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
27.053362171950916

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S,7R)-7-hexyl-5-hydroxy-3-(hydroxymethyl)-2,3,6,7-tetrahydro-1,4-oxazepin-2-one

> <ALOGPS_LOGP>
1.06

> <JCHEM_LOGP>
1.8144373433333323

> <ALOGPS_LOGS>
-2.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.855139792982463

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.4342138781927805

> <JCHEM_PKA_STRONGEST_BASIC>
0.6986023603831807

> <JCHEM_POLAR_SURFACE_AREA>
79.12000000000002

> <JCHEM_REFRACTIVITY>
62.26270000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.26e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,7R)-7-hexyl-5-hydroxy-3-(hydroxymethyl)-6,7-dihydro-3H-1,4-oxazepin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 14-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-21         0                                  
HETATM    1  C   UNK     0      -4.101  -5.602   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.767  -6.372   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.434  -5.602   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.100  -6.372   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.234  -5.602   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.568  -6.372   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.786  -4.066   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.744  -4.467   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.901  -5.602   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.208  -4.582   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.915  -3.019   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.645  -6.016   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       6.438  -3.249   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0       9.412  -3.080   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       4.461  -1.547   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       7.693  -7.145   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       5.174  -6.470   0.000  0.00  0.00           O+0
HETATM   18  H   UNK     0       3.844  -7.141   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       8.122  -5.821   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    9                                                       
CONECT    7    9   11                                                       
CONECT    8   10   14                                                       
CONECT    9    6    7   17   18                                             
CONECT   10    8   12   13   19                                             
CONECT   11    7   13   15                                                  
CONECT   12   10   16   17                                                  
CONECT   13   10   11                                                       
CONECT   14    8                                                            
CONECT   15   11                                                            
CONECT   16   12                                                            
CONECT   17    9   12                                                       
CONECT   18    9                                                            
CONECT   19   10                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   38    0
END

Synonyms

Not Available

Molecular Formula

C₁₂H₂₁NO₄

Average Mass

243.303

Monoisotopic Mass

243.14705816

IUPAC Name

(3S,7R)-7-hexyl-5-hydroxy-3-(hydroxymethyl)-2,3,6,7-tetrahydro-1,4-oxazepin-2-one

Traditional Name

(3S,7R)-7-hexyl-5-hydroxy-3-(hydroxymethyl)-6,7-dihydro-3H-1,4-oxazepin-2-one

CAS Registry Number

Not Available

SMILES

[H][C@@]1(CCCCCC)CC(O)=N[C@@]([H])(CO)C(=O)O1

InChI Identifier

InChI=1S/C12H21NO4/c1-2-3-4-5-6-9-7-11(15)13-10(8-14)12(16)17-9/h9-10,14H,2-8H2,1H3,(H,13,15)/t9-,10+/m1/s1

InChI Key

STXCXCAUQNUQQP-ZJUUUORDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acid esters. These are ester derivatives of alpha amino acids.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acid esters

Alternative Parents

Substituents

Alpha-amino acid ester
Para-oxazepine
Carboxamide group
Carboxylic acid ester
Lactam
Lactone
Secondary carboxylic acid amide
Oxacycle
Monocarboxylic acid or derivatives
Azacycle
Organoheterocyclic compound
Organonitrogen compound
Alcohol
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Carbonyl group
Organooxygen compound
Primary alcohol
Organic oxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	1.26 g/L	ALOGPS
logP	1.06	ALOGPS
logP	1.81	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	5.43	ChemAxon
pKa (Strongest Basic)	0.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	79.12 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	62.26 m³·mol⁻¹	ChemAxon
Polarizability	27.05 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-09	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

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	200.6
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	50.4
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	410.0
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	421.4
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	443.6
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-23	251.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	1676.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	117.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	337.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	321.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	139.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	170.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	137.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	55.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	332.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	197.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	336.9
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1228.3
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	932.3

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	Serratin_TMS_1	CCCCCC[C@@H]1CC(O[Si](C)(C)C)=N[C@@H](CO)C(=O)O1	standard non polar	2025-10-23	1797.33
Gas Chromatography	Serratin_TMS_2	CCCCCC[C@@H]1CC(O)=N[C@@H](CO[Si](C)(C)C)C(=O)O1	standard non polar	2025-10-23	1784.73
Gas Chromatography	Serratin_TMS_3	CCCCCC[C@@H]1CC(O[Si](C)(C)C)=N[C@@H](CO[Si](C)(C)C)C(=O)O1	standard non polar	2025-10-23	1957.75
Gas Chromatography	Serratin_TMS_1	CCCCCC[C@@H]1CC(O[Si](C)(C)C)=N[C@@H](CO)C(=O)O1	standard polar	2025-10-23	2290.82
Gas Chromatography	Serratin_TMS_2	CCCCCC[C@@H]1CC(O)=N[C@@H](CO[Si](C)(C)C)C(=O)O1	standard polar	2025-10-23	2133.26
Gas Chromatography	Serratin_TMS_3	CCCCCC[C@@H]1CC(O[Si](C)(C)C)=N[C@@H](CO[Si](C)(C)C)C(=O)O1	standard polar	2025-10-23	2165.35

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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	Proteobacteria	1	Human	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

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

78436146

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139583806

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 Serratin (MMDBc0003321)

MOL for #<Metabolite:0x00007f9abc264630>

3D MOL for #<Metabolite:0x00007f9abc264630>

3D SDF for #<Metabolite:0x00007f9abc264630>

3D-SDF for #<Metabolite:0x00007f9abc264630>

PDB for #<Metabolite:0x00007f9abc264630>

3D PDB for #<Metabolite:0x00007f9abc264630>

SMILES for #<Metabolite:0x00007f9abc264630>

INCHI for #<Metabolite:0x00007f9abc264630>

Structure for #<Metabolite:0x00007f9abc264630>

3D Structure for #<Metabolite:0x00007f9abc264630>