NP-MRD: Showing NP-Card for n-[(3s)-2-oxooxolan-3-yl]hexanimidic acid (NP0143898)

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Record Information

Version

2.0

Created at

2022-09-01 22:45:11 UTC

Updated at

2022-09-01 22:45:11 UTC

NP-MRD ID

NP0143898

Secondary Accession Numbers

None

Natural Product Identification

Common Name

n-[(3s)-2-oxooxolan-3-yl]hexanimidic acid

Description

N-hexanoyl-homoserine lactone, also known as HHL-serine or C6-AHL, belongs to the class of organic compounds known as n-acyl-alpha amino acids and derivatives. N-acyl-alpha amino acids and derivatives are compounds containing an alpha amino acid (or a derivative thereof) which bears an acyl group at its terminal nitrogen atom. Thus, N-hexanoyl-homoserine lactone is considered to be a fatty amide lipid molecule. n-[(3s)-2-oxooxolan-3-yl]hexanimidic acid is found in Azospirillum lipoferum. N-hexanoyl-homoserine lactone is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 31 31  0  0  0  0  0  0  0  0999 V2000
   -5.2136   -0.3243   -0.2020 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8386   -0.9043    0.0989 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8398    0.2292   -0.1540 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4176   -0.2668    0.1258 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5002    0.8869   -0.1408 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9266    0.5523    0.0904 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8368    1.5748   -0.1371 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3479   -0.5791    0.4719 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7419   -0.8229    0.6726 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5827   -0.5819   -0.5431 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7427    0.2174   -0.0226 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2129    0.9054    1.0768 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3006    0.0859    1.6931 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9762    0.0820    2.8997 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2466    0.7148    0.1572 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0236   -0.9325    0.2792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4136   -0.3564   -1.2910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7880   -1.1100    1.1878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6008   -1.7705   -0.5217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1173    1.0288    0.5626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9188    0.6293   -1.1743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3559   -0.5066    1.2137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2115   -1.1679   -0.4474 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5927    1.1803   -1.2066 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7900    1.7297    0.4930 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6210    2.5521   -0.1114 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8993   -1.8701    1.0358 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0778   -0.0087   -1.3274 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9387   -1.5572   -0.9795 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5057   -0.5082    0.3451 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1578    0.8985   -0.8010 H   0  0  0  0  0  0  0  0  0  0  0  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
  9  8  1  0
  8  6  2  0
  6  7  1  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  1  0
 13  9  1  0
  9 27  1  1
 10 28  1  0
 10 29  1  0
 11 30  1  0
 11 31  1  0
  7 26  1  0
  5 24  1  0
  5 25  1  0
  4 22  1  0
  4 23  1  0
  3 20  1  0
  3 21  1  0
  2 18  1  0
  2 19  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
M  END

  Mrv0541 05041405172D          

 15 15  0  0  1  0            999 V2000
   -3.2588    3.9207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5443    4.3332    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8298    3.9207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1154    4.3332    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4009    3.9207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4962    3.9977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0482    4.6108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7425    4.3332    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3136    4.3332    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8287    5.1537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0280    3.9207    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3136    5.1582    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2157    5.7057    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6357    5.3252    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7857    3.5094    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
  7  6  1  0  0  0  0
  8  6  1  0  0  0  0
  9  5  1  0  0  0  0
 10  8  1  0  0  0  0
  8 11  1  6  0  0  0
 11  9  2  0  0  0  0
  9 12  1  4  0  0  0
 13 10  2  0  0  0  0
 14  7  1  0  0  0  0
 14 10  1  0  0  0  0
  8 15  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0143898

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(CCOC1=O)N=C(O)CCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C10H17NO3/c1-2-3-4-5-9(12)11-8-6-7-14-10(8)13/h8H,2-7H2,1H3,(H,11,12)/t8-/m0/s1

> <INCHI_KEY>
ZJFKKPDLNLCPNP-QMMMGPOBSA-N

> <FORMULA>
C10H17NO3

> <MOLECULAR_WEIGHT>
199.2469

> <EXACT_MASS>
199.120843415

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
21.482039767487514

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
N-[(3S)-2-oxooxolan-3-yl]hexanimidic acid

> <ALOGPS_LOGP>
1.85

> <JCHEM_LOGP>
1.771502154333334

> <ALOGPS_LOGS>
-2.25

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.588803180572699

> <JCHEM_PKA_STRONGEST_BASIC>
1.5177650020916063

> <JCHEM_POLAR_SURFACE_AREA>
58.89

> <JCHEM_REFRACTIVITY>
51.80960000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.13e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[(3S)-2-oxooxolan-3-yl]hexanimidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   15  H   UNK     0       0.000   0.000   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    9                                                       
CONECT    6    7    8                                                       
CONECT    7    6   14                                                       
CONECT    8    6   10   11   15                                             
CONECT    9    5   11   12                                                  
CONECT   10    8   13   14                                                  
CONECT   11    8    9                                                       
CONECT   12    9                                                            
CONECT   13   10                                                            
CONECT   14    7   10                                                       
CONECT   15    8                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol

Synonyms

Value	Source
HHL-Serine	MeSH
C6-AHL	MeSH
N-[(3S)-2-Oxooxolan-3-yl]hexanimidate	Generator

Chemical Formula

C₁₀H₁₇NO₃

Average Mass

199.2469 Da

Monoisotopic Mass

199.12084 Da

IUPAC Name

N-[(3S)-2-oxooxolan-3-yl]hexanimidic acid

Traditional Name

N-[(3S)-2-oxooxolan-3-yl]hexanimidic acid

CAS Registry Number

Not Available

SMILES

[H][C@@]1(CCOC1=O)N=C(O)CCCCC

InChI Identifier

InChI=1S/C10H17NO3/c1-2-3-4-5-9(12)11-8-6-7-14-10(8)13/h8H,2-7H2,1H3,(H,11,12)/t8-/m0/s1

InChI Key

ZJFKKPDLNLCPNP-QMMMGPOBSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Azospirillum lipoferum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as n-acyl-alpha amino acids and derivatives. N-acyl-alpha amino acids and derivatives are compounds containing an alpha amino acid (or a derivative thereof) which bears an acyl group at its terminal nitrogen atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

N-acyl-alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid ester
N-acyl-alpha amino acid or derivatives
Acyl-homoserine lactone
Acyl-l-homoserine lactone
Fatty amide
Gamma butyrolactone
N-acyl-amine
Fatty acyl
Oxolane
Secondary carboxylic acid amide
Lactone
Carboxylic acid ester
Carboxamide group
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Oxacycle
Organooxygen compound
Organonitrogen compound
Organic oxide
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	1.85	ALOGPS
logP	1.77	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	7.59	ChemAxon
pKa (Strongest Basic)	1.52	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	58.89 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	51.81 m³·mol⁻¹	ChemAxon
Polarizability	21.48 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

10058590

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for n-[(3s)-2-oxooxolan-3-yl]hexanimidic acid (NP0143898)

MOL for NP0143898 (n-[(3s)-2-oxooxolan-3-yl]hexanimidic acid)

3D MOL for NP0143898 (n-[(3s)-2-oxooxolan-3-yl]hexanimidic acid)

3D SDF for NP0143898 (n-[(3s)-2-oxooxolan-3-yl]hexanimidic acid)

3D-SDF for NP0143898 (n-[(3s)-2-oxooxolan-3-yl]hexanimidic acid)

PDB for NP0143898 (n-[(3s)-2-oxooxolan-3-yl]hexanimidic acid)

3D PDB for NP0143898 (n-[(3s)-2-oxooxolan-3-yl]hexanimidic acid)

SMILES for NP0143898 (n-[(3s)-2-oxooxolan-3-yl]hexanimidic acid)

INCHI for NP0143898 (n-[(3s)-2-oxooxolan-3-yl]hexanimidic acid)

Structure for NP0143898 (n-[(3s)-2-oxooxolan-3-yl]hexanimidic acid)

3D Structure for NP0143898 (n-[(3s)-2-oxooxolan-3-yl]hexanimidic acid)