MiMeDB: Showing metabocard for Syringolide 1 (MMDBc0002608)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-14 20:54:15 UTC

Update Date

2025-10-07 16:04:36 UTC

Metabolite ID

MMDBc0002608

Metabolite Identification

Common Name

Syringolide 1

Description

Syringolide 1 is a phytotoxin belonging to the class of plant metabolites known as syringolides. This compound has been shown to interact specifically with soluble proteins in soybean leaf extracts, with a notable binding affinity characterized by a Kd value of 8.7 nM (PMID:12237390 ). The binding activity is attributed to a 34-kDa protein isolated using a syringolide affinity-gel column (PMID:9501258 ). Notably, syringolide 1 does not exhibit ligand-specific binding to the microsomal fraction of these extracts (PMID:12237390 ). Furthermore, competition studies indicate a direct correlation between the binding affinity of syringolide 1 and its elicitor activity, suggesting its role in plant defense mechanisms (PMID:12237390 ). In biological assays, syringolide 1 has been demonstrated to trigger significant physiological responses, such as Ca2+ influx, K+ efflux, and extracellular alkalization in soybean cells that carry the disease-resistance gene Rpg4, while showing no effect in rpg4 cultivars (PMID:12226392 ). These findings highlight the potential role of syringolide 1 in mediating plant defense responses against pathogens.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305142122542D          

 22 24  0  0  1  0            999 V2000
   -2.5566    2.6939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8421    2.2814    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1277    2.6939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4132    2.2814    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3013    2.6939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4993    2.8093    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9564    1.5898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8862    3.3613    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6288    1.7293    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1718    2.9488    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8004    0.9224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3433    2.1418    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0157    2.2814    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9725    4.1818    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2483    0.3093    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5308    1.6139    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6208    0.8361    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1638    2.0556    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3513    3.0351    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1943    3.8106    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9144    1.3168    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9255    2.6133    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
  8  6  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12  7  1  0  0  0  0
 12  9  1  0  0  0  0
 12 10  1  0  0  0  0
 13  5  1  1  0  0  0
 13  9  1  0  0  0  0
  8 14  1  6  0  0  0
 15 11  2  0  0  0  0
 13 16  1  6  0  0  0
 17  7  1  0  0  0  0
 17 11  1  0  0  0  0
 18  6  1  0  0  0  0
 12 18  1  1  0  0  0
 19 10  1  0  0  0  0
 19 13  1  0  0  0  0
  8 20  1  1  0  0  0
  9 21  1  1  0  0  0
 10 22  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0002608

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C13H20O6/c1-2-3-4-5-13(16)9-11(15)17-7-12(9)10(19-13)8(14)6-18-12/h8-10,14,16H,2-7H2,1H3/t8-,9+,10+,12+,13-/m1/s1

> <INCHI_KEY>
KFHLOSLXXIXBMW-YTCQTTRASA-N

> <FORMULA>
C13H20O6

> <MOLECULAR_WEIGHT>
272.297

> <EXACT_MASS>
272.125988364

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
27.59906257988277

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
0.77

> <JCHEM_LOGP>
0.6435921496666661

> <ALOGPS_LOGS>
-1.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.33240516743075

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.472876206725692

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5345050818872528

> <JCHEM_POLAR_SURFACE_AREA>
85.22000000000001

> <JCHEM_REFRACTIVITY>
63.27500000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.55e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,4R,5S,7R,8S)-4,7-dihydroxy-7-pentyl-2,6,10-trioxatricyclo[6.3.0.0^{1,5}]undecan-9-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      -4.772   5.029   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.439   4.259   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.105   5.029   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.771   4.259   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.562   5.029   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.532   5.244   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.519   2.968   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.388   6.274   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.040   3.228   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.054   5.504   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.361   1.722   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.374   3.998   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.896   4.259   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       5.549   7.806   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       2.330   0.577   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.991   3.013   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       4.892   1.561   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       5.906   3.837   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       2.522   5.665   0.000  0.00  0.00           O+0
HETATM   20  H   UNK     0       4.096   7.113   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       1.707   2.458   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       5.461   4.878   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   13                                                       
CONECT    6    8   18                                                       
CONECT    7   12   17                                                       
CONECT    8    6   10   14   20                                             
CONECT    9   11   12   13   21                                             
CONECT   10    8   12   19   22                                             
CONECT   11    9   15   17                                                  
CONECT   12    7    9   10   18                                             
CONECT   13    5    9   16   19                                             
CONECT   14    8                                                            
CONECT   15   11                                                            
CONECT   16   13                                                            
CONECT   17    7   11                                                       
CONECT   18    6   12                                                       
CONECT   19   10   13                                                       
CONECT   20    8                                                            
CONECT   21    9                                                            
CONECT   22   10                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

Synonyms

Not Available

Molecular Formula

C₁₃H₂₀O₆

Average Mass

272.297

Monoisotopic Mass

272.125988364

IUPAC Name

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

Traditional Name

(1R,4R,5S,7R,8S)-4,7-dihydroxy-7-pentyl-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)(CCCCC)O[C@@]13[H]

InChI Identifier

InChI=1S/C13H20O6/c1-2-3-4-5-13(16)9-11(15)17-7-12(9)10(19-13)8(14)6-18-12/h8-10,14,16H,2-7H2,1H3/t8-,9+,10+,12+,13-/m1/s1

InChI Key

KFHLOSLXXIXBMW-YTCQTTRASA-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	25.5 g/L	ALOGPS
logP	0.77	ALOGPS
logP	0.64	ChemAxon
logS	-1	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	4	ChemAxon
Refractivity	63.28 m³·mol⁻¹	ChemAxon
Polarizability	27.6 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	No	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

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank

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

C00000378

Chemspider ID

9922401

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11747697

PDB ID

Not Available

ChEBI ID

Not Available

CMMC Knowledgebase

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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 1 (MMDBc0002608)

MOL for #<Metabolite:0x00007fd409013b70>

3D MOL for #<Metabolite:0x00007fd409013b70>

3D SDF for #<Metabolite:0x00007fd409013b70>

3D-SDF for #<Metabolite:0x00007fd409013b70>

PDB for #<Metabolite:0x00007fd409013b70>

3D PDB for #<Metabolite:0x00007fd409013b70>

SMILES for #<Metabolite:0x00007fd409013b70>

INCHI for #<Metabolite:0x00007fd409013b70>

Structure for #<Metabolite:0x00007fd409013b70>

3D Structure for #<Metabolite:0x00007fd409013b70>