NP-MRD: Showing NP-Card for Fragin (NP0350930)

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Record Information

Version

2.0

Created at

2025-04-11 20:45:19 UTC

Updated at

2025-07-30 03:35:08 UTC

NP-MRD ID

NP0350930

Natural Product DOI

https://doi.org/10.57994/3915

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Fragin

Description

Fragin was first documented in 2018 (PMID: 29602945). Based on a literature review a significant number of articles have been published on Fragin (PMID: 31945256) (PMID: 34594316) (PMID: 34659189) (PMID: 32212725) (PMID: 39702669) (PMID: 38651488).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 01222323112D          

 19 18  0  0  0  0            999 V2000
    0.6139   -5.8901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -6.4302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0171   -6.1602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6407   -6.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4202   -6.4302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0439   -6.9703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8234   -6.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4471   -7.2404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2912   -8.0505    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2266   -6.9703    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.8503   -7.5104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6298   -7.2404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7857   -6.4302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1621   -5.8901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5653   -6.1602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2535   -7.7805    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    9.0330   -7.5104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.1889   -6.7003    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0976   -8.5906    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  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
 13 15  1  0  0  0  0
 12 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 16 19  1  0  0  0  0
M  CHG  2  16   1  19  -1
M  END
> <DATABASE_ID>
NP0350930

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCCC(=O)NCC(C(C)C)[N+](\[O-])=N/O

> <INCHI_IDENTIFIER>
InChI=1/C13H27N3O3/c1-4-5-6-7-8-9-13(17)14-10-12(11(2)3)16(19)15-18/h11-12,18H,4-10H2,1-3H3,(H,14,17)/b16-15+

> <INCHI_KEY>
SXMAXSCAVUEAAA-FOCLMDBBNA-N

> <FORMULA>
C13H27N3O3

> <MOLECULAR_WEIGHT>
273.377

> <EXACT_MASS>
273.205241741

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
46

> <JCHEM_AVERAGE_POLARIZABILITY>
31.187134400153504

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(E)-(hydroxyimino)(3-methyl-1-octanamidobutan-2-yl)oxidoazanium

> <JCHEM_LOGP>
1.2213503785282545

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.417828686476282

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.068263622650672

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2052609991718177

> <JCHEM_POLAR_SURFACE_AREA>
87.76

> <JCHEM_REFRACTIVITY>
75.8592

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(E)-(hydroxyimino)(3-methyl-1-octanamidobutan-2-yl)oxidoazanium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-JAN-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-JAN-23         0                                  
HETATM    1  C   UNK     0       1.146 -10.995   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310 -12.003   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.765 -11.499   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.929 -12.507   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.384 -12.003   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.549 -13.011   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.004 -12.507   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.168 -13.515   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       9.877 -15.028   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0      11.623 -13.011   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      12.787 -14.019   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      14.242 -13.515   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      14.533 -12.003   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      13.369 -10.995   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      15.989 -11.499   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0      15.406 -14.524   0.000  0.00  0.00           N+1
HETATM   17  N   UNK     0      16.862 -14.019   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0      17.153 -12.507   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      15.115 -16.036   0.000  0.00  0.00           O-1
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   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   16                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   12   17   19                                                  
CONECT   17   16   18                                                       
CONECT   18   17                                                            
CONECT   19   16                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   36    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₂₇N₃O₃

Average Mass

273.3770 Da

Monoisotopic Mass

273.20524 Da

IUPAC Name

(E)-(hydroxyimino)(3-methyl-1-octanamidobutan-2-yl)oxidoazanium

Traditional Name

(E)-(hydroxyimino)(3-methyl-1-octanamidobutan-2-yl)oxidoazanium

CAS Registry Number

Not Available

SMILES

CCCCCCCC(=O)NCC(C(C)C)[N+](\[O-])=N/O

InChI Identifier

InChI=1/C13H27N3O3/c1-4-5-6-7-8-9-13(17)14-10-12(11(2)3)16(19)15-18/h11-12,18H,4-10H2,1-3H3,(H,14,17)/b16-15+

InChI Key

SXMAXSCAVUEAAA-FOCLMDBBNA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CDCl3, experimental)	Not Available	Georgia Institute of Technology	Jiangpeiyun Jin	2025-04-11	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Burkholderia cenocepacia		Not Available

Chemical Taxonomy

Classification

Not classified

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	1.22	ChemAxon
pKa (Strongest Acidic)	4.07	ChemAxon
pKa (Strongest Basic)	-1.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	87.76 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	75.86 m³·mol⁻¹	ChemAxon
Polarizability	31.19 Å³	ChemAxon
Number of Rings	0	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

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Jenul C, Sieber S, Daeppen C, Mathew A, Lardi M, Pessi G, Hoepfner D, Neuburger M, Linden A, Gademann K, Eberl L: Biosynthesis of fragin is controlled by a novel quorum sensing signal. Nat Commun. 2018 Mar 30;9(1):1297. doi: 10.1038/s41467-018-03690-2. [PubMed:29602945 ]
Sieber S, Daeppen C, Jenul C, Mannancherril V, Eberl L, Gademann K: Biosynthesis and Structure-Activity Relationship Investigations of the Diazeniumdiolate Antifungal Agent Fragin. Chembiochem. 2020 Jun 2;21(11):1587-1592. doi: 10.1002/cbic.201900755. Epub 2020 Mar 4. [PubMed:31945256 ]
Zhou L, de Jong A, Yi Y, Kuipers OP: Identification, Isolation, and Characterization of Medipeptins, Antimicrobial Peptides From Pseudomonas mediterranea EDOX. Front Microbiol. 2021 Sep 14;12:732771. doi: 10.3389/fmicb.2021.732771. eCollection 2021. [PubMed:34594316 ]
Nascimento FX, Uron P, Glick BR, Giachini A, Rossi MJ: Genomic Analysis of the 1-Aminocyclopropane-1-Carboxylate Deaminase-Producing Pseudomonas thivervalensis SC5 Reveals Its Multifaceted Roles in Soil and in Beneficial Interactions With Plants. Front Microbiol. 2021 Sep 30;12:752288. doi: 10.3389/fmicb.2021.752288. eCollection 2021. [PubMed:34659189 ]
McAvoy AC, Jaiyesimi O, Threatt PH, Seladi T, Goldberg JB, da Silva RR, Garg N: Differences in Cystic Fibrosis-Associated Burkholderia spp. Bacteria Metabolomes after Exposure to the Antibiotic Trimethoprim. ACS Infect Dis. 2020 May 8;6(5):1154-1168. doi: 10.1021/acsinfecdis.9b00513. Epub 2020 Apr 1. [PubMed:32212725 ]
Ren J, Mathew A, Rodriguez-Garcia M, Kohler T, Blacque O, Linden A, Eberl L, Sieber S, Gademann K: Functional biosynthetic stereodivergence in a gene cluster via a dihydrosydnone N-oxide. Commun Chem. 2024 Dec 19;7(1):301. doi: 10.1038/s42004-024-01372-3. [PubMed:39702669 ]
Rabico F, Borelli TC, Alnoch RC, Polizeli MLTM, da Silva RR, Silva-Rocha R, Guazzaroni ME: Novel Pseudomonas Species Prevent the Growth of the Phytopathogenic Fungus Aspergillus flavus. BioTech (Basel). 2024 Mar 30;13(2):8. doi: 10.3390/biotech13020008. [PubMed:38651488 ]

Showing NP-Card for Fragin (NP0350930)

MOL for NP0350930 (Fragin)

3D MOL for NP0350930 (Fragin)

3D SDF for NP0350930 (Fragin)

3D-SDF for NP0350930 (Fragin)

PDB for NP0350930 (Fragin)

3D PDB for NP0350930 (Fragin)

SMILES for NP0350930 (Fragin)

INCHI for NP0350930 (Fragin)

Structure for NP0350930 (Fragin)

3D Structure for NP0350930 (Fragin)