NP-MRD: Showing NP-Card for Autoinducer II (NP0003983)

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Record Information

Version

1.0

Created at

2020-12-09 01:30:49 UTC

Updated at

2021-07-15 16:47:55 UTC

NP-MRD ID

NP0003983

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Autoinducer II

Provided By

NPAtlas

Description

Autoinducer-2 is also known as AI-2. Autoinducer-2 is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Autoinducer II is found in Vibrio harveyi. It was first documented in 2002 (PMID: 11823863). Based on a literature review a significant number of articles have been published on autoinducer-2 (PMID: 23078586) (PMID: 23305926) (PMID: 23649272) (PMID: 24026770).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242118033D          

 23 24  0  0  0  0            999 V2000
   -0.3427   -1.6089    1.4268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4373   -0.2698    0.7825 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6583    0.3388    0.9423 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0589    0.8665   -0.2627 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7742    1.0520   -1.0665 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9870    1.1706   -2.4061 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1051   -0.2781   -0.6856 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7123   -1.3162   -1.3678 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2442   -0.1999   -0.8334 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7271    0.3959    0.3979 B   0  5  2  0  0  4  0  0  0  0  0  0
    2.2958    1.7280    0.1128 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7788   -0.4926    0.9374 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6032    0.5315    1.3014 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5314   -2.1628    1.0833 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2402   -2.2281    1.2699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1998   -1.4527    2.5356 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6241    0.0575   -0.8119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6397    1.7930   -0.1868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2293    1.8763   -0.5919 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4061    1.9306   -2.7345 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7114   -2.1744   -0.8708 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1597    1.8202    0.5505 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7861   -1.3776    0.4775 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  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
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 10 12  1  0  0  0  0
 10 13  1  0  0  0  0
  7  2  1  0  0  0  0
 13  2  1  0  0  0  0
  1 14  1  0  0  0  0
  1 15  1  0  0  0  0
  1 16  1  0  0  0  0
  4 17  1  0  0  0  0
  4 18  1  0  0  0  0
  5 19  1  1  0  0  0
  6 20  1  0  0  0  0
  8 21  1  0  0  0  0
 11 22  1  0  0  0  0
 12 23  1  0  0  0  0
M  CHG  1  10  -1
M  END
> <DATABASE_ID>
NP0003983

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@@]1([H])C([H])([H])O[C@@]2(O[B-](O[H])(O[H])O[C@]12O[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C5H10BO7/c1-4-5(8,3(7)2-11-4)13-6(9,10)12-4/h3,7-10H,2H2,1H3/q-1/t3-,4+,5+/m0/s1

> <INCHI_KEY>
ACKRRKSNOOISSG-VPENINKCSA-N

> <FORMULA>
C5H10BO7

> <MOLECULAR_WEIGHT>
192.94

> <EXACT_MASS>
193.05195814

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
16.268331196742572

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyl-tetrahydro-2H-furo[2,3-d][1,3,2]dioxaborol-2-uide

> <ALOGPS_LOGP>
-1.25

> <JCHEM_LOGP>
-3.2504999999999997

> <ALOGPS_LOGS>
-0.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.262903760794945

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.88658968571494

> <JCHEM_PKA_STRONGEST_BASIC>
-3.9291094245979368

> <JCHEM_POLAR_SURFACE_AREA>
108.61000000000001

> <JCHEM_REFRACTIVITY>
33.18789999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.07e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
autoinducer-2

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0      -0.343  -1.609   1.427  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.437  -0.270   0.783  0.00  0.00           C+0
HETATM    3  O   UNK     0      -1.658   0.339   0.942  0.00  0.00           O+0
HETATM    4  C   UNK     0      -2.059   0.867  -0.263  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.774   1.052  -1.067  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.987   1.171  -2.406  0.00  0.00           O+0
HETATM    7  C   UNK     0      -0.105  -0.278  -0.686  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.712  -1.316  -1.368  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.244  -0.200  -0.833  0.00  0.00           O+0
HETATM   10  B   UNK     0       1.727   0.396   0.398  0.00  0.00           B-1
HETATM   11  O   UNK     0       2.296   1.728   0.113  0.00  0.00           O+0
HETATM   12  O   UNK     0       2.779  -0.493   0.937  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.603   0.532   1.301  0.00  0.00           O+0
HETATM   14  H   UNK     0       0.531  -2.163   1.083  0.00  0.00           H+0
HETATM   15  H   UNK     0      -1.240  -2.228   1.270  0.00  0.00           H+0
HETATM   16  H   UNK     0      -0.200  -1.453   2.536  0.00  0.00           H+0
HETATM   17  H   UNK     0      -2.624   0.058  -0.812  0.00  0.00           H+0
HETATM   18  H   UNK     0      -2.640   1.793  -0.187  0.00  0.00           H+0
HETATM   19  H   UNK     0      -0.229   1.876  -0.592  0.00  0.00           H+0
HETATM   20  H   UNK     0      -0.406   1.931  -2.735  0.00  0.00           H+0
HETATM   21  H   UNK     0      -0.711  -2.174  -0.871  0.00  0.00           H+0
HETATM   22  H   UNK     0       3.160   1.820   0.551  0.00  0.00           H+0
HETATM   23  H   UNK     0       2.786  -1.378   0.478  0.00  0.00           H+0
CONECT    1    2   14   15   16                                             
CONECT    2    1    3    7   13                                             
CONECT    3    2    4                                                       
CONECT    4    3    5   17   18                                             
CONECT    5    4    6    7   19                                             
CONECT    6    5   20                                                       
CONECT    7    5    8    9    2                                             
CONECT    8    7   21                                                       
CONECT    9    7   10                                                       
CONECT   10    9   11   12   13                                             
CONECT   11   10   22                                                       
CONECT   12   10   23                                                       
CONECT   13   10    2                                                       
CONECT   14    1                                                            
CONECT   15    1                                                            
CONECT   16    1                                                            
CONECT   17    4                                                            
CONECT   18    4                                                            
CONECT   19    5                                                            
CONECT   20    6                                                            
CONECT   21    8                                                            
CONECT   22   11                                                            
CONECT   23   12                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
(3AS,6S,6ar)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-D][1,3,2]dioxaborolan-2-uide	ChEBI
AI-2	ChEBI
Autoinducer 2	ChEBI
AI-2 autoinducer	MeSH
N-Octanoyl-HSL	MeSH
N-Octanoyl-L-homoserine lactone	MeSH
N-Octanoylhomoserine lactone	MeSH
VAI-2	MeSH
C8HSL Compound	MeSH

Chemical Formula

C₅H₁₀BO₇

Average Mass

192.9400 Da

Monoisotopic Mass

193.05196 Da

IUPAC Name

(3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyl-tetrahydro-2H-furo[2,3-d][1,3,2]dioxaborol-2-uide

Traditional Name

autoinducer-2

CAS Registry Number

Not Available

SMILES

C[C@]12OC[C@H](O)[C@@]1(O)O[B-](O)(O)O2

InChI Identifier

InChI=1S/C5H10BO7/c1-4-5(8,3(7)2-11-4)13-6(9,10)12-4/h3,7-10H,2H2,1H3/q-1/t3-,4+,5+/m0/s1

InChI Key

ACKRRKSNOOISSG-VPENINKCSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Vibrio harveyi	NPAtlas	11823863

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as monosaccharides. These are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Monosaccharides

Alternative Parents

Substituents

Monosaccharide
Tetrahydrofuran
Organic tetrahydroxyborate
1,3,2-dioxaborolane
Secondary alcohol
Organic borate
Oxacycle
Organic metalloid salt
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Organic salt
Alcohol
Organic anion
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

organic anion (CHEBI:40646 )

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	-1.2	ALOGPS
logP	-3.3	ChemAxon
logS	-0.47	ALOGPS
pKa (Strongest Acidic)	9.89	ChemAxon
pKa (Strongest Basic)	-3.9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	108.61 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	33.19 m³·mol⁻¹	ChemAxon
Polarizability	16.27 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA028590

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

393894

KEGG Compound ID

C16421

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Autoinducer-2

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

40646

Good Scents ID

Not Available

References

General References

Chen X, Schauder S, Potier N, Van Dorsselaer A, Pelczer I, Bassler BL, Hughson FM: Structural identification of a bacterial quorum-sensing signal containing boron. Nature. 2002 Jan 31;415(6871):545-9. doi: 10.1038/415545a. [PubMed:11823863 ]
Niu C, Robbins CM, Pittman KJ, Osborn jL, Stubblefield BA, Simmons RB, Gilbert ES: LuxS influences Escherichia coli biofilm formation through autoinducer-2-dependent and autoinducer-2-independent modalities. FEMS Microbiol Ecol. 2013 Mar;83(3):778-91. doi: 10.1111/1574-6941.12034. Epub 2012 Nov 26. [PubMed:23078586 ]
Blair WM, Doucette GJ: The Vibrio harveyi bioassay used routinely to detect AI-2 quorum sensing inhibition is confounded by inconsistent normalization across marine matrices. J Microbiol Methods. 2013 Mar;92(3):250-2. doi: 10.1016/j.mimet.2012.12.023. Epub 2013 Jan 7. [PubMed:23305926 ]
Karim MM, Nagao A, Mansur FJ, Matsunaga T, Akakabe Y, Noiri Y, Ebisu S, Kato A, Azakami H: The periodontopathogenic bacterium Eikenella corrodens produces an autoinducer-2-inactivating enzyme. Biosci Biotechnol Biochem. 2013;77(5):1080-5. doi: 10.1271/bbb.130047. Epub 2013 May 7. [PubMed:23649272 ]
Peixoto RJ, Miranda KR, Ferreira EO, de Paula GR, Rocha ER, Lobo LA, Domingues RM: Production of AI-2 is mediated by the S-ribosylhomocystein lyase gene luxS in Bacteroides fragilis and Bacteroides vulgatus. J Basic Microbiol. 2014 Jul;54(7):644-9. doi: 10.1002/jobm.201300311. Epub 2013 Sep 11. [PubMed:24026770 ]

Showing NP-Card for Autoinducer II (NP0003983)

MOL for NP0003983 (Autoinducer II)

3D MOL for NP0003983 (Autoinducer II)

3D SDF for NP0003983 (Autoinducer II)

3D-SDF for NP0003983 (Autoinducer II)

PDB for NP0003983 (Autoinducer II)

3D PDB for NP0003983 (Autoinducer II)

SMILES for NP0003983 (Autoinducer II)

INCHI for NP0003983 (Autoinducer II)

Structure for NP0003983 (Autoinducer II)

3D Structure for NP0003983 (Autoinducer II)