NP-MRD: Showing NP-Card for (-)-Syringolide 1 (NP0050302)

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Record Information

Version

2.0

Created at

2022-04-27 20:52:00 UTC

Updated at

2022-04-27 20:52:00 UTC

NP-MRD ID

NP0050302

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Syringolide 1

Description

Syringolide 1 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. (-)-Syringolide 1 is found in Pseudomonas syringae and Pseudomonas syringae pv.tomato. (-)-Syringolide 1 was first documented in 1996 (PMID: 12226392). Based on a literature review a small amount of articles have been published on Syringolide 1 (PMID: 9501258) (PMID: 12237390).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304272222522D          

 19 21  0  0  1  0            999 V2000
   -1.5823    1.8457    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9635    1.3001    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0411    0.4788    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2533    1.7201    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4333    2.5252    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2547    2.6029    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2768    2.9452    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8956    2.3996    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5680    1.6425    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2825    1.2300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9969    1.6425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7114    1.2300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4259    1.6425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1403    1.2300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5853    0.8176    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0968    3.7503    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7245    3.8280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0522    3.0708    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6424    4.3692    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  4  2  1  1  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  8  9  1  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  9 15  1  1  0  0  0
  7 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
  5 18  1  6  0  0  0
 16 19  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0050302

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCC[C@@]1(O)O[C@H]2[C@H](O)CO[C@]22COC(=O)[C@H]12

> <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                                 27-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-APR-22         0                                  
HETATM    1  O   UNK     0      -2.954   3.445   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.798   2.427   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -1.943   0.894   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -0.473   3.211   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.809   4.714   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.342   4.859   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.517   5.498   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.672   4.479   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.060   3.066   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.394   2.296   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.728   3.066   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.061   2.296   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.395   3.066   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.729   2.296   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       1.093   1.526   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       0.181   7.001   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.352   7.146   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -1.964   5.732   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       1.199   8.156   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    9                                                  
CONECT    5    4    6    7   18                                             
CONECT    6    5    1                                                       
CONECT    7    5    8   16                                                  
CONECT    8    7    9                                                       
CONECT    9    8    4   10   15                                             
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15    9                                                            
CONECT   16    7   17   19                                                  
CONECT   17   16   18                                                       
CONECT   18   17    5                                                       
CONECT   19   16                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₂₀O₆

Average Mass

272.2970 Da

Monoisotopic Mass

272.12599 Da

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

CCCCC[C@@]1(O)O[C@H]2[C@H](O)CO[C@]22COC(=O)[C@H]12

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

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Pseudomonas syringae	LOTUS Database	35616633
Pseudomonas syringae pv.tomato	Bacteria	KNApSAcK

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

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

Good Scents ID

Not Available

References

General References

Ji C, Boyd C, Slaymaker D, Okinaka Y, Takeuchi Y, Midland SL, Sims JJ, Herman E, Keen N: Characterization of a 34-kDa soybean binding protein for the syringolide elicitors. Proc Natl Acad Sci U S A. 1998 Mar 17;95(6):3306-11. doi: 10.1073/pnas.95.6.3306. [PubMed:9501258 ]
Ji C, Okinaka Y, Takeuchi Y, Tsurushima T, Buzzell RI, Sims JJ, Midland SL, Slaymaker D, Yoshikawa M, Yamaoka N, Keen NT: Specific Binding of the Syringolide Elicitors to a Soluble Protein Fraction from Soybean Leaves. Plant Cell. 1997 Aug;9(8):1425-1433. doi: 10.1105/tpc.9.8.1425. [PubMed:12237390 ]
Atkinson MM, Midland SL, Sims JJ, Keen NT: Syringolide 1 Triggers Ca2+ Influx, K+ Efflux, and Extracellular Alkalization in Soybean Cells Carrying the Disease-Resistance Gene Rpg4. Plant Physiol. 1996 Sep;112(1):297-302. doi: 10.1104/pp.112.1.297. [PubMed:12226392 ]

Showing NP-Card for (-)-Syringolide 1 (NP0050302)

MOL for NP0050302 ((-)-Syringolide 1)

3D MOL for NP0050302 ((-)-Syringolide 1)

3D SDF for NP0050302 ((-)-Syringolide 1)

3D-SDF for NP0050302 ((-)-Syringolide 1)

PDB for NP0050302 ((-)-Syringolide 1)

3D PDB for NP0050302 ((-)-Syringolide 1)

SMILES for NP0050302 ((-)-Syringolide 1)

INCHI for NP0050302 ((-)-Syringolide 1)

Structure for NP0050302 ((-)-Syringolide 1)

3D Structure for NP0050302 ((-)-Syringolide 1)