NP-MRD: Showing NP-Card for carboxynorspermidine (NP0198519)

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Record Information

Version

2.0

Created at

2022-09-04 16:59:03 UTC

Updated at

2022-09-04 16:59:04 UTC

NP-MRD ID

NP0198519

Secondary Accession Numbers

None

Natural Product Identification

Common Name

carboxynorspermidine

Description

Carboxynorspermidine belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. carboxynorspermidine is found in Apis cerana. carboxynorspermidine was first documented in 2009 (PMID: 19196710). Based on a literature review a small amount of articles have been published on carboxynorspermidine (PMID: 22239666) (PMID: 22025614) (PMID: 20534592).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 29 28  0  0  0  0  0  0  0  0999 V2000
    4.1026   -0.8556   -0.2355 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9614   -0.1735    0.3422 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3474    0.6788   -0.7218 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1520    1.4485   -0.2725 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0757    0.6003    0.1982 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0691    1.3303    0.6281 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1433    0.4298    1.0993 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7169   -0.5393    0.1322 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.7552   -1.2809    0.8942 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8219   -1.5447   -0.4239 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9075   -2.7817   -0.0944 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8063   -1.2846   -1.3488 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4339   -0.4438   -1.1143 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8223   -1.1167    0.4427 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2356    0.3854    1.2353 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2201   -0.9804    0.5984 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0951    0.0653   -1.6053 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0992    1.4306   -1.0848 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4042    2.2201    0.4631 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7486    1.9850   -1.1709 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3828   -0.1313    0.8439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7396    1.9352    1.5256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4053    2.0976   -0.1008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0149    1.0516    1.4711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7853   -0.0794    2.0320 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2676   -0.0588   -0.6924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2547   -2.0362    1.4235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4136   -1.7238    0.2394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9798   -0.6276   -2.1167 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
  8 10  1  0
 10 12  1  0
 10 11  2  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  2 16  1  0
  3 17  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  8 26  1  6
  9 27  1  0
  9 28  1  0
 12 29  1  0
M  END

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  N   UNK     0       4.263   4.001   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       5.596   4.771   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       9.597   4.001   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      10.931   4.771   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.265   4.001   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      13.598   6.311   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      16.266   4.771   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      14.932   2.461   0.000  0.00  0.00           O+0
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   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₇H₁₇N₃O₂

Average Mass

175.2320 Da

Monoisotopic Mass

175.13208 Da

IUPAC Name

(2S)-2-amino-4-[(3-aminopropyl)amino]butanoic acid

Traditional Name

(2S)-2-amino-4-[(3-aminopropyl)amino]butanoic acid

CAS Registry Number

Not Available

SMILES

NCCCNCC[C@H](N)C(O)=O

InChI Identifier

InChI=1S/C7H17N3O2/c8-3-1-4-10-5-2-6(9)7(11)12/h6,10H,1-5,8-9H2,(H,11,12)/t6-/m0/s1

InChI Key

KFJYMJZJSUORBX-LURJTMIESA-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
Apis cerana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-alpha-amino acids

Alternative Parents

Substituents

L-alpha-amino acid
Amino fatty acid
Fatty acyl
Fatty acid
Amino acid
Carboxylic acid
Secondary aliphatic amine
Monocarboxylic acid or derivatives
Secondary amine
Amine
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Organic oxide
Primary aliphatic amine
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Organic nitrogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

non-proteinogenic L-alpha-amino acid (CHEBI:67204 )

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	-4.5	ChemAxon
pKa (Strongest Acidic)	2.71	ChemAxon
pKa (Strongest Basic)	10.33	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	101.37 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	46.15 m³·mol⁻¹	ChemAxon
Polarizability	19.54 Å³	ChemAxon
Number of Rings	0	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

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

28533159

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

70678631

PDB ID

Not Available

ChEBI ID

67204

Good Scents ID

Not Available

References

General References

Parker ZM, Pendergraft SS, Sobieraj J, McGinnis MM, Karatan E: Elevated levels of the norspermidine synthesis enzyme NspC enhance Vibrio cholerae biofilm formation without affecting intracellular norspermidine concentrations. FEMS Microbiol Lett. 2012 Apr;329(1):18-27. doi: 10.1111/j.1574-6968.2012.02498.x. Epub 2012 Jan 30. [PubMed:22239666 ]
Hanfrey CC, Pearson BM, Hazeldine S, Lee J, Gaskin DJ, Woster PM, Phillips MA, Michael AJ: Alternative spermidine biosynthetic route is critical for growth of Campylobacter jejuni and is the dominant polyamine pathway in human gut microbiota. J Biol Chem. 2011 Dec 16;286(50):43301-12. doi: 10.1074/jbc.M111.307835. Epub 2011 Oct 24. [PubMed:22025614 ]
Deng X, Lee J, Michael AJ, Tomchick DR, Goldsmith EJ, Phillips MA: Evolution of substrate specificity within a diverse family of beta/alpha-barrel-fold basic amino acid decarboxylases: X-ray structure determination of enzymes with specificity for L-arginine and carboxynorspermidine. J Biol Chem. 2010 Aug 13;285(33):25708-19. doi: 10.1074/jbc.M110.121137. Epub 2010 Jun 8. [PubMed:20534592 ]
Lee J, Sperandio V, Frantz DE, Longgood J, Camilli A, Phillips MA, Michael AJ: An alternative polyamine biosynthetic pathway is widespread in bacteria and essential for biofilm formation in Vibrio cholerae. J Biol Chem. 2009 Apr 10;284(15):9899-907. doi: 10.1074/jbc.M900110200. Epub 2009 Feb 5. [PubMed:19196710 ]
LOTUS database [Link]

Showing NP-Card for carboxynorspermidine (NP0198519)

MOL for NP0198519 (carboxynorspermidine)

3D MOL for NP0198519 (carboxynorspermidine)

3D SDF for NP0198519 (carboxynorspermidine)

3D-SDF for NP0198519 (carboxynorspermidine)

PDB for NP0198519 (carboxynorspermidine)

3D PDB for NP0198519 (carboxynorspermidine)

SMILES for NP0198519 (carboxynorspermidine)

INCHI for NP0198519 (carboxynorspermidine)

Structure for NP0198519 (carboxynorspermidine)

3D Structure for NP0198519 (carboxynorspermidine)