NP-MRD: Showing NP-Card for [(1-hydroxynonylidene)amino]acetic acid (NP0165459)

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Record Information

Version

2.0

Created at

2022-09-03 00:36:40 UTC

Updated at

2022-09-03 00:36:40 UTC

NP-MRD ID

NP0165459

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(1-hydroxynonylidene)amino]acetic acid

Description

N-Nonanoylglycine, also known as acylglycine c:9, Belongs to the class of organic compounds known as n-acyl-alpha amino acids. N-acyl-alpha amino acids are compounds containing an alpha amino acid which bears an acyl group at its terminal nitrogen atom. [(1-hydroxynonylidene)amino]acetic acid is found in Trypanosoma brucei. N-Nonanoylglycine is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 35  0  0  0  0  0  0  0  0999 V2000
    3.2789   -1.4726    2.2401 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8219   -1.6123    0.8329 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0004   -2.5895    0.0269 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5681   -2.1405   -0.0695 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5240   -0.7987   -0.7426 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0463   -0.3717   -0.8306 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0567    0.9709   -1.5089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2841    1.5861   -1.7073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9451    1.8272   -0.4130 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3944    1.5962    0.6708 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2842    2.3529   -0.4485 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9378    2.5915    0.8122 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0579    1.3270    1.6089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6181    0.2540    1.1545 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6724    1.4244    2.8489 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5489   -0.6438    2.3212 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1634   -1.2524    2.8964 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8200   -2.4353    2.5468 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8568   -2.0423    0.8463 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9105   -0.6417    0.3411 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0988   -3.6024    0.4692 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4457   -2.5870   -1.0050 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9493   -2.8643   -0.6220 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1343   -2.0590    0.9638 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8731   -0.8358   -1.7885 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0773   -0.0165   -0.2200 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4437   -1.1564   -1.4770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4062   -0.3857    0.1738 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5916    0.8173   -2.4850 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7304    1.6194   -0.8708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1090    2.5481   -2.2655 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8894    0.8860   -2.3237 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7794    2.5594   -1.3360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9299    3.0561    0.6390 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3030    3.2841    1.4391 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4421    0.8074    3.0784 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 13 15  1  0
 13 14  2  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  2 19  1  0
  2 20  1  0
  3 21  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  6 27  1  0
  6 28  1  0
  7 29  1  0
  7 30  1  0
  8 31  1  0
  8 32  1  0
 11 33  1  0
 12 34  1  0
 12 35  1  0
 15 36  1  0
M  END

  Mrv1652303102016512D          

 15 14  0  0  0  0            999 V2000
    8.6857  -14.9258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4001  -14.5133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1146  -14.9258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8291  -14.5133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5435  -14.9258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2580  -14.5133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9725  -14.9258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6870  -14.5133    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.9725  -15.7508    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9712  -14.5133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1159  -14.5133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1159  -13.6883    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.8304  -14.9258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.4015  -14.9258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2567  -14.9258    0.0000 C   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
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  7  2  0  0  0  0
 10  1  1  0  0  0  0
 12 11  2  0  0  0  0
 13 11  1  0  0  0  0
 14 11  1  0  0  0  0
 14  8  1  0  0  0  0
 15 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0165459

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCCCC(=O)NCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H21NO3/c1-2-3-4-5-6-7-8-10(13)12-9-11(14)15/h2-9H2,1H3,(H,12,13)(H,14,15)

> <INCHI_KEY>
JXDFEUKNHBHUCP-UHFFFAOYSA-N

> <FORMULA>
C11H21NO3

> <MOLECULAR_WEIGHT>
215.2893

> <EXACT_MASS>
215.152143543

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
24.96132416246347

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-nonanamidoacetic acid

> <ALOGPS_LOGP>
2.58

> <JCHEM_LOGP>
2.039318882999999

> <ALOGPS_LOGS>
-2.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
16.17245199590322

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.046618031970887

> <JCHEM_PKA_STRONGEST_BASIC>
-1.6781963755392004

> <JCHEM_POLAR_SURFACE_AREA>
66.4

> <JCHEM_REFRACTIVITY>
57.680099999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.55e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
nonanamidoacetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-MAR-20         0                                  
HETATM    1  C   UNK     0      16.213 -27.861   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      17.547 -27.091   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      18.881 -27.861   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      20.214 -27.091   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      21.548 -27.861   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      22.882 -27.091   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      24.215 -27.861   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      25.549 -27.091   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0      24.215 -29.401   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      14.880 -27.091   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      28.216 -27.091   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      28.216 -25.551   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      29.550 -27.861   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      26.883 -27.861   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      13.546 -27.861   0.000  0.00  0.00           C+0
CONECT    1    2   10                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7   14                                                       
CONECT    9    7                                                            
CONECT   10    1   15                                                       
CONECT   11   12   13   14                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11    8                                                       
CONECT   15   10                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

View in JSmol

Synonyms

Value	Source
Acylglycine c:9	ChEBI
Nonanoylglycine	HMDB

Chemical Formula

C₁₁H₂₁NO₃

Average Mass

215.2893 Da

Monoisotopic Mass

215.15214 Da

IUPAC Name

2-nonanamidoacetic acid

Traditional Name

nonanamidoacetic acid

CAS Registry Number

Not Available

SMILES

CCCCCCCCC(=O)NCC(O)=O

InChI Identifier

InChI=1S/C11H21NO3/c1-2-3-4-5-6-7-8-10(13)12-9-11(14)15/h2-9H2,1H3,(H,12,13)(H,14,15)

InChI Key

JXDFEUKNHBHUCP-UHFFFAOYSA-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
Trypanosoma brucei	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as n-acyl-alpha amino acids. N-acyl-alpha amino acids are compounds containing an alpha amino acid 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

Alternative Parents

Substituents

N-acyl-alpha-amino acid
Fatty amide
N-acyl-amine
Fatty acyl
Carboxamide group
Secondary carboxylic acid amide
Carboxylic acid
Monocarboxylic acid or derivatives
Carbonyl group
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

fatty amide (CHEBI:74439 )
N-acylglycine (CHEBI:74439 )

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	2.58	ALOGPS
logP	2.04	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	4.05	ChemAxon
pKa (Strongest Basic)	-1.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.4 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	57.68 m³·mol⁻¹	ChemAxon
Polarizability	24.96 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

HMDB0013279

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB029362

KNApSAcK ID

Not Available

Chemspider ID

8352257

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10176752

PDB ID

Not Available

ChEBI ID

74439

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(1-hydroxynonylidene)amino]acetic acid (NP0165459)

MOL for NP0165459 ([(1-hydroxynonylidene)amino]acetic acid)

3D MOL for NP0165459 ([(1-hydroxynonylidene)amino]acetic acid)

3D SDF for NP0165459 ([(1-hydroxynonylidene)amino]acetic acid)

3D-SDF for NP0165459 ([(1-hydroxynonylidene)amino]acetic acid)

PDB for NP0165459 ([(1-hydroxynonylidene)amino]acetic acid)

3D PDB for NP0165459 ([(1-hydroxynonylidene)amino]acetic acid)

SMILES for NP0165459 ([(1-hydroxynonylidene)amino]acetic acid)

INCHI for NP0165459 ([(1-hydroxynonylidene)amino]acetic acid)

Structure for NP0165459 ([(1-hydroxynonylidene)amino]acetic acid)

3D Structure for NP0165459 ([(1-hydroxynonylidene)amino]acetic acid)