MiMeDB: Showing metabocard for Syringolide 2 (MMDBc0019773)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 09:48:20 UTC

Update Date

2025-10-07 16:07:01 UTC

Metabolite ID

MMDBc0019773

Metabolite Identification

Common Name

Syringolide 2

Description

Syringolide 2 is a member of the chemical class of phytotoxins, specifically categorized as a plant elicitor derived from the bacterial pathogen Pseudomonas syringae. Its chemical structure features a complex arrangement of carbon, hydrogen, and oxygen atoms that contribute to its bioactivity. As a signaling molecule, Syringolide 2 plays a crucial role in plant-pathogen interactions, triggering defense responses in host plants. Upon recognition by plant receptors, it activates various signaling pathways, including the salicylic acid-mediated defense pathway, which leads to the expression of pathogenesis-related genes and the synthesis of protective compounds. This compound exemplifies the intricate chemical warfare between plants and pathogens, showcasing how microbial metabolites can manipulate host physiology. The study of Syringolide 2 not only enhances our understanding of plant immunity but also provides insights into the chemical ecology of plant-microbe interactions (PMID:10959854 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152111482D          

 24 26  0  0  1  0            999 V2000
   -3.5128    3.7558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7983    3.3433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0838    3.7558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3694    3.3433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6549    3.7558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0596    3.3433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7741    3.7558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9721    3.8712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4292    2.6517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3590    4.4232    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1016    2.7913    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6446    4.0107    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2732    1.9843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8161    3.2038    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4885    3.3433    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4453    5.2437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7211    1.3712    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0036    2.6759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0936    1.8981    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6366    3.1175    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8241    4.0970    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6671    4.8726    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3872    2.3788    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3982    3.6752    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
 10  8  1  0  0  0  0
 12 10  1  0  0  0  0
 13 11  1  0  0  0  0
 14  9  1  0  0  0  0
 14 11  1  0  0  0  0
 14 12  1  0  0  0  0
 15  7  1  1  0  0  0
 15 11  1  0  0  0  0
 10 16  1  6  0  0  0
 17 13  2  0  0  0  0
 15 18  1  6  0  0  0
 19  9  1  0  0  0  0
 19 13  1  0  0  0  0
 20  8  1  0  0  0  0
 14 20  1  1  0  0  0
 21 12  1  0  0  0  0
 21 15  1  0  0  0  0
 10 22  1  1  0  0  0
 11 23  1  1  0  0  0
 12 24  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0019773

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(O)CO[C@@]23COC(=O)[C@]2([H])[C@@](O)(CCCCCCC)O[C@@]13[H]

> <INCHI_IDENTIFIER>
InChI=1S/C15H24O6/c1-2-3-4-5-6-7-15(18)11-13(17)19-9-14(11)12(21-15)10(16)8-20-14/h10-12,16,18H,2-9H2,1H3/t10-,11+,12+,14+,15-/m1/s1

> <INCHI_KEY>
ILUIUWLXEYGVIK-FUQNVFFISA-N

> <FORMULA>
C15H24O6

> <MOLECULAR_WEIGHT>
300.351

> <EXACT_MASS>
300.157288493

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
45

> <JCHEM_AVERAGE_POLARIZABILITY>
31.861751581937583

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,4R,5S,7R,8S)-7-heptyl-4,7-dihydroxy-2,6,10-trioxatricyclo[6.3.0.0^{1,5}]undecan-9-one

> <ALOGPS_LOGP>
1.51

> <JCHEM_LOGP>
1.5327294796666648

> <ALOGPS_LOGS>
-1.60

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.332405164540543

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.472876012281485

> <JCHEM_PKA_STRONGEST_BASIC>
-3.534505081887257

> <JCHEM_POLAR_SURFACE_AREA>
85.22000000000001

> <JCHEM_REFRACTIVITY>
72.477

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.52e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,4R,5S,7R,8S)-7-heptyl-4,7-dihydroxy-2,6,10-trioxatricyclo[6.3.0.0^{1,5}]undecan-9-one

> <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      -6.557   7.011   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.223   6.241   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.890   7.011   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.556   6.241   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.222   7.011   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.111   6.241   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.445   7.011   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.415   7.226   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.401   4.950   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.270   8.257   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.923   5.210   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.937   7.487   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.243   3.704   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.257   5.980   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.779   6.241   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       6.431   9.788   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       3.213   2.560   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       1.873   4.995   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       5.775   3.543   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       6.788   5.819   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       3.405   7.648   0.000  0.00  0.00           O+0
HETATM   22  H   UNK     0       4.979   9.095   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       2.589   4.440   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       6.343   6.860   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   15                                                       
CONECT    8   10   20                                                       
CONECT    9   14   19                                                       
CONECT   10    8   12   16   22                                             
CONECT   11   13   14   15   23                                             
CONECT   12   10   14   21   24                                             
CONECT   13   11   17   19                                                  
CONECT   14    9   11   12   20                                             
CONECT   15    7   11   18   21                                             
CONECT   16   10                                                            
CONECT   17   13                                                            
CONECT   18   15                                                            
CONECT   19    9   13                                                       
CONECT   20    8   14                                                       
CONECT   21   12   15                                                       
CONECT   22   10                                                            
CONECT   23   11                                                            
CONECT   24   12                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   52    0
END

Synonyms

Not Available

Molecular Formula

C₁₅H₂₄O₆

Average Mass

300.351

Monoisotopic Mass

300.157288493

IUPAC Name

(1R,4R,5S,7R,8S)-7-heptyl-4,7-dihydroxy-2,6,10-trioxatricyclo[6.3.0.0^{1,5}]undecan-9-one

Traditional Name

(1R,4R,5S,7R,8S)-7-heptyl-4,7-dihydroxy-2,6,10-trioxatricyclo[6.3.0.0^{1,5}]undecan-9-one

CAS Registry Number

Not Available

SMILES

[H][C@@]1(O)CO[C@@]23COC(=O)[C@]2([H])[C@@](O)(CCCCCCC)O[C@@]13[H]

InChI Identifier

InChI=1S/C15H24O6/c1-2-3-4-5-6-7-15(18)11-13(17)19-9-14(11)12(21-15)10(16)8-20-14/h10-12,16,18H,2-9H2,1H3/t10-,11+,12+,14+,15-/m1/s1

InChI Key

ILUIUWLXEYGVIK-FUQNVFFISA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as furofurans. These are organic compounds containing a two furan rings fused to each other. Furan is a five-membered aromatic ring with four carbon atoms and one oxygen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Furofurans

Sub Class

Not Available

Direct Parent

Furofurans

Alternative Parents

Substituents

Furofuran
Gamma butyrolactone
Monosaccharide
Oxolane
Carboxylic acid ester
Hemiacetal
Lactone
Secondary alcohol
Monocarboxylic acid or derivatives
Ether
Dialkyl ether
Oxacycle
Carboxylic acid derivative
Carbonyl group
Organic oxide
Organic oxygen compound
Alcohol
Hydrocarbon derivative
Organooxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	7.52 g/L	ALOGPS
logP	1.51	ALOGPS
logP	1.53	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	11.47	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	85.22 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	72.48 m³·mol⁻¹	ChemAxon
Polarizability	31.86 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Not Available

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		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

9132768

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10957551

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 Syringolide 2 (MMDBc0019773)

MOL for #<Metabolite:0x00007f8de9a76100>

3D MOL for #<Metabolite:0x00007f8de9a76100>

3D SDF for #<Metabolite:0x00007f8de9a76100>

3D-SDF for #<Metabolite:0x00007f8de9a76100>

PDB for #<Metabolite:0x00007f8de9a76100>

3D PDB for #<Metabolite:0x00007f8de9a76100>

SMILES for #<Metabolite:0x00007f8de9a76100>

INCHI for #<Metabolite:0x00007f8de9a76100>

Structure for #<Metabolite:0x00007f8de9a76100>

3D Structure for #<Metabolite:0x00007f8de9a76100>