MiMeDB: Showing metabocard for (S)-N-dodecanoyl-HSL (MMDBc0012142)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 03:46:12 UTC

Update Date

2025-10-07 16:05:57 UTC

Metabolite ID

MMDBc0012142

Metabolite Identification

Common Name

(S)-N-dodecanoyl-HSL

Description

(S)-N-dodecanoyl-HSL is a member of the acyl-homoserine lactones (acyl-HSLs) chemical class, which are signaling molecules involved in quorum sensing among bacteria. This metabolite has been identified in a chemical study focused on acyl-HSLs produced by Enterobacter sakazakii, alongside other related compounds such as (S)-N-heptanoyl-HSL and (S)-N-tetradecanoyl-HSL (PMID:22132860 ). The biological significance of (S)-N-dodecanoyl-HSL is underscored by its role in bacterial communication and regulation of gene expression in response to population density. Furthermore, the biotransformation of (S)-N-dodecanoyl-HSL has been investigated, revealing its conversion into (S)-N-dodecanoyl-homoserine, dodecanoic acid, and homoserine in the presence of Bacillus species, highlighting its potential metabolic pathways and interactions in microbial ecosystems (PMID:22132860 ). This compound exemplifies the complexity of bacterial communication and its implications for understanding microbial behavior and interactions.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152105462D          

 21 21  0  0  1  0            999 V2000
   -5.0024    7.8369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2879    8.2494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5735    7.8369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8590    8.2494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1445    7.8369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4300    8.2494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7156    7.8369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0011    8.2494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7134    7.8369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4278    8.2494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1423    7.8369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0394    7.9139    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5914    8.5270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2857    8.2494    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8568    8.2494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3720    9.0699    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5713    7.8369    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8568    9.0744    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7589    9.6220    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1789    9.2414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5938    8.6988    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
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  9  1  0  0  0  0
 11 10  1  0  0  0  0
 13 12  1  0  0  0  0
 14 12  1  0  0  0  0
 15 11  1  0  0  0  0
 16 14  1  0  0  0  0
 14 17  1  6  0  0  0
 17 15  2  0  0  0  0
 15 18  1  4  0  0  0
 19 16  2  0  0  0  0
 20 13  1  0  0  0  0
 20 16  1  0  0  0  0
 14 21  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0012142

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(CCOC1=O)N=C(O)CCCCCCCCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C16H29NO3/c1-2-3-4-5-6-7-8-9-10-11-15(18)17-14-12-13-20-16(14)19/h14H,2-13H2,1H3,(H,17,18)/t14-/m0/s1

> <INCHI_KEY>
WILLZMOKUUPJSL-AWEZNQCLSA-N

> <FORMULA>
C16H29NO3

> <MOLECULAR_WEIGHT>
283.412

> <EXACT_MASS>
283.214743798

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
34.119316243414225

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
N-[(3S)-2-oxooxolan-3-yl]dodecanimidic acid

> <ALOGPS_LOGP>
4.84

> <JCHEM_LOGP>
4.438914144333334

> <ALOGPS_LOGS>
-4.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.956019385637912

> <JCHEM_PKA_STRONGEST_BASIC>
1.5494394655223853

> <JCHEM_POLAR_SURFACE_AREA>
58.89

> <JCHEM_REFRACTIVITY>
79.41559999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.14e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[(3S)-2-oxooxolan-3-yl]dodecanimidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0      -9.338  14.629   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -8.004  15.399   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -6.670  14.629   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.337  15.399   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.003  14.629   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.669  15.399   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.336  14.629   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.002  15.399   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.332  14.629   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.665  15.399   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.999  14.629   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.407  14.773   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.437  15.917   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.000  15.399   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.333  15.399   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.161  16.931   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       6.666  14.629   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0       5.333  16.939   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       7.017  17.961   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       9.667  17.251   0.000  0.00  0.00           O+0
HETATM   21  H   UNK     0       6.708  16.238   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    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   15                                                       
CONECT   12   13   14                                                       
CONECT   13   12   20                                                       
CONECT   14   12   16   17   21                                             
CONECT   15   11   17   18                                                  
CONECT   16   14   19   20                                                  
CONECT   17   14   15                                                       
CONECT   18   15                                                            
CONECT   19   16                                                            
CONECT   20   13   16                                                       
CONECT   21   14                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

Synonyms

Not Available

Molecular Formula

C₁₆H₂₉NO₃

Average Mass

283.412

Monoisotopic Mass

283.214743798

IUPAC Name

N-[(3S)-2-oxooxolan-3-yl]dodecanimidic acid

Traditional Name

N-[(3S)-2-oxooxolan-3-yl]dodecanimidic acid

CAS Registry Number

Not Available

SMILES

[H][C@@]1(CCOC1=O)N=C(O)CCCCCCCCCCC

InChI Identifier

InChI=1S/C16H29NO3/c1-2-3-4-5-6-7-8-9-10-11-15(18)17-14-12-13-20-16(14)19/h14H,2-13H2,1H3,(H,17,18)/t14-/m0/s1

InChI Key

WILLZMOKUUPJSL-AWEZNQCLSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as n-acyl-alpha amino acids and derivatives. N-acyl-alpha amino acids and derivatives are compounds containing an alpha amino acid (or a derivative thereof) which bears an acyl group at its terminal nitrogen atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

N-acyl-alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid ester
N-acyl-alpha amino acid or derivatives
Acyl-homoserine lactone
Acyl-l-homoserine lactone
Fatty amide
Gamma butyrolactone
N-acyl-amine
Fatty acyl
Oxolane
Secondary carboxylic acid amide
Lactone
Carboxylic acid ester
Carboxamide group
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Oxacycle
Organooxygen compound
Organonitrogen compound
Organic oxide
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Carbonyl group
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	0.0041 g/L	ALOGPS
logP	4.84	ALOGPS
logP	4.44	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	5.96	ChemAxon
pKa (Strongest Basic)	1.55	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	58.89 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	79.42 m³·mol⁻¹	ChemAxon
Polarizability	34.12 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

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	155.9
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (void)	2025-10-23	32.3
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	536.5
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	741.9
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	728.1
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (retained)	2025-10-23	369.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	2586.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	89.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	299.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	568.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	303.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	196.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	192.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (void)	2025-10-23	15.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (void)	2025-10-23	419.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	494.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	422.8
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1580.6
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	1549.9

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	(S)-N-dodecanoyl-HSL_TMS_1	CCCCCCCCCCCC(=N[C@H]1CCOC1=O)O[Si](C)(C)C	standard non polar	2025-10-23	2240.03
Gas Chromatography	(S)-N-dodecanoyl-HSL_TMS_1	CCCCCCCCCCCC(=N[C@H]1CCOC1=O)O[Si](C)(C)C	standard polar	2025-10-23	2120.4

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 ; Human feces	Metabolic reconstruction
Bacteria	Proteobacteria	1	Human ; Human feces	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

8396929

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10221437

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

WILLZMOKUUPJSL-AWEZNQCLSA-N

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 (S)-N-dodecanoyl-HSL (MMDBc0012142)

MOL for #<Metabolite:0x00007f2dfd0905b0>

3D MOL for #<Metabolite:0x00007f2dfd0905b0>

3D SDF for #<Metabolite:0x00007f2dfd0905b0>

3D-SDF for #<Metabolite:0x00007f2dfd0905b0>

PDB for #<Metabolite:0x00007f2dfd0905b0>

3D PDB for #<Metabolite:0x00007f2dfd0905b0>

SMILES for #<Metabolite:0x00007f2dfd0905b0>

INCHI for #<Metabolite:0x00007f2dfd0905b0>

Structure for #<Metabolite:0x00007f2dfd0905b0>

3D Structure for #<Metabolite:0x00007f2dfd0905b0>