NP-MRD: Showing NP-Card for Small bacteriocin (NP0335193)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2024-09-11 00:28:44 UTC

Updated at

2024-09-11 00:28:45 UTC

NP-MRD ID

NP0335193

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Small bacteriocin

Description

Small bacteriocin was first documented in 2008 (PMID: 18402461). Based on a literature review a small amount of articles have been published on Small bacteriocin (PMID: 21821958) (PMID: 38301890) (PMID: 26442036) (PMID: 18172715).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 05262303002D          

 23 23  0  0  0  0            999 V2000
   -3.5488   -1.5322    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0337   -2.1996    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8587   -2.1996    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1137   -2.9842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4462   -3.4691    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7788   -2.9842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9942   -3.2392    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7238   -1.5322    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3113   -0.8177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3113   -2.2466    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4863   -0.8177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0738   -0.1032    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2488   -0.1032    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1637    0.6113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9887    0.6113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4012    1.3257    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2262    1.3257    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6387    2.0402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4637    2.0402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8762    2.7547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7012    2.7547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1137    3.4691    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0738   -1.5322    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  6  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  2  0  0  0  0
  1  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
  9 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
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 11 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0335193

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCC\C=C\CCCC(O)CC(=O)NC1CCOC1=O

> <INCHI_IDENTIFIER>
InChI=1/C18H31NO4/c1-2-3-4-5-6-7-8-9-10-11-15(20)14-17(21)19-16-12-13-23-18(16)22/h7-8,15-16,20H,2-6,9-14H2,1H3,(H,19,21)/b8-7+

> <INCHI_KEY>
GFSFGXWHLLUVRK-BQYQJAHWNA-N

> <FORMULA>
C18H31NO4

> <MOLECULAR_WEIGHT>
325.449

> <EXACT_MASS>
325.225308482

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
38.099360836938914

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(7E)-3-hydroxy-N-(2-oxooxolan-3-yl)tetradec-7-enamide

> <JCHEM_LOGP>
2.9157146236666662

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.230350297973967

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.40465508558505

> <JCHEM_PKA_STRONGEST_BASIC>
-1.890988835336276

> <JCHEM_POLAR_SURFACE_AREA>
75.63

> <JCHEM_REFRACTIVITY>
90.72800000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(7E)-3-hydroxy-N-(2-oxooxolan-3-yl)tetradec-7-enamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-23         0                                  
HETATM    1  N   UNK     0      -6.624  -2.860   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -7.530  -4.106   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -9.070  -4.106   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -9.546  -5.571   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -8.300  -6.476   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -7.054  -5.571   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -5.589  -6.047   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -5.084  -2.860   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.314  -1.526   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -4.314  -4.194   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -2.774  -1.526   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.004  -0.193   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.464  -0.193   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.306   1.141   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.846   1.141   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.616   2.475   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.156   2.475   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.926   3.808   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.466   3.808   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.236   5.142   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.776   5.142   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.546   6.476   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -2.004  -2.860   0.000  0.00  0.00           O+0
CONECT    1    2    8                                                       
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    2    5    7                                                  
CONECT    7    6                                                            
CONECT    8    1    9   10                                                  
CONECT    9    8   11                                                       
CONECT   10    8                                                            
CONECT   11    9   12   23                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21                                                            
CONECT   23   11                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   46    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₈H₃₁NO₄

Average Mass

325.4490 Da

Monoisotopic Mass

325.22531 Da

IUPAC Name

(7E)-3-hydroxy-N-(2-oxooxolan-3-yl)tetradec-7-enamide

Traditional Name

(7E)-3-hydroxy-N-(2-oxooxolan-3-yl)tetradec-7-enamide

CAS Registry Number

Not Available

SMILES

CCCCCC\C=C\CCCC(O)CC(=O)NC1CCOC1=O

InChI Identifier

InChI=1/C18H31NO4/c1-2-3-4-5-6-7-8-9-10-11-15(20)14-17(21)19-16-12-13-23-18(16)22/h7-8,15-16,20H,2-6,9-14H2,1H3,(H,19,21)/b8-7+

InChI Key

GFSFGXWHLLUVRK-BQYQJAHWNA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

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	2.92	ChemAxon
pKa (Strongest Acidic)	12.4	ChemAxon
pKa (Strongest Basic)	-1.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	75.63 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	90.73 m³·mol⁻¹	ChemAxon
Polarizability	38.1 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

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

Yajima A: Synthesis of microbial signaling molecules and their stereochemistry-activity relationships. Biosci Biotechnol Biochem. 2011;75(8):1418-29. doi: 10.1271/bbb.110283. Epub 2011 Aug 7. [PubMed:21821958 ]
Zhao X, Wang W, Zeng X, Xu R, Yuan B, Yu W, Wang M, Jia R, Chen S, Zhu D, Liu M, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Sun D, Cheng A: Klebicin E, a pore-forming bacteriocin of Klebsiella pneumoniae, exploits the porin OmpC and the Ton system for translocation. J Biol Chem. 2024 Mar;300(3):105694. doi: 10.1016/j.jbc.2024.105694. Epub 2024 Jan 30. [PubMed:38301890 ]
Smith DL, Praslickova D, Ilangumaran G: Inter-organismal signaling and management of the phytomicrobiome. Front Plant Sci. 2015 Sep 14;6:722. doi: 10.3389/fpls.2015.00722. eCollection 2015. [PubMed:26442036 ]
Yajima A, van Brussel AA, Schripsema J, Nukada T, Yabuta G: Synthesis and stereochemistry-activity relationship of small bacteriocin, an autoinducer of the symbiotic nitrogen-fixing bacterium Rhizobium leguminosarum. Org Lett. 2008 May 15;10(10):2047-50. doi: 10.1021/ol8005198. Epub 2008 Apr 11. [PubMed:18402461 ]
Pascual LM, Daniele MB, Giordano W, Pajaro MC, Barberis IL: Purification and partial characterization of novel bacteriocin L23 produced by Lactobacillus fermentum L23. Curr Microbiol. 2008 Apr;56(4):397-402. doi: 10.1007/s00284-007-9094-4. Epub 2008 Jan 3. [PubMed:18172715 ]

Showing NP-Card for Small bacteriocin (NP0335193)

MOL for NP0335193 (Small bacteriocin)

3D MOL for NP0335193 (Small bacteriocin)

3D SDF for NP0335193 (Small bacteriocin)

3D-SDF for NP0335193 (Small bacteriocin)

PDB for NP0335193 (Small bacteriocin)

3D PDB for NP0335193 (Small bacteriocin)

SMILES for NP0335193 (Small bacteriocin)

INCHI for NP0335193 (Small bacteriocin)

Structure for NP0335193 (Small bacteriocin)

3D Structure for NP0335193 (Small bacteriocin)