NP-MRD: Showing NP-Card for N2-Succinyl-L-ornithine (NP0086726)

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Record Information

Version

1.0

Created at

2022-05-11 16:29:17 UTC

Updated at

2022-05-11 16:29:18 UTC

NP-MRD ID

NP0086726

Secondary Accession Numbers

None

Natural Product Identification

Common Name

N2-Succinyl-L-ornithine

Description

N2-Succinyl-L-ornithine 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. N2-Succinyl-L-ornithine is a very strong basic compound (based on its pKa). N2-Succinyl-L-ornithine is found in Trypanosoma brucei. N2-Succinyl-L-ornithine exists in all living organisms, ranging from bacteria to humans.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 31  0  0  0  0  0  0  0  0999 V2000
   -5.1065   -0.3819    0.0147 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7870   -0.0505    0.6081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8088   -1.0043    0.0387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4069   -0.9404    0.4528 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5786    0.2565    0.1819 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7656   -0.0926    0.7567 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8627   -0.2479   -0.1135 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7182   -0.0973   -1.3414 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1804   -0.5895    0.4425 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1882   -0.6286   -0.6752 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2581    0.7150   -1.2961 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5664    1.6450   -0.8218 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0824    0.9649   -2.4023 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9730    1.5209    0.7906 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7702    1.7779    2.0020 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5907    2.5021    0.0378 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5090   -1.2020    0.4896 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7678    0.4093    0.1180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8455   -0.1941    1.7083 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6627    1.0037    0.4223 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2021   -2.0405    0.3151 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8522   -1.0270   -1.0848 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8997   -1.8688    0.0196 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3815   -1.2027    1.5698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4225    0.3272   -0.9143 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8656   -0.2126    1.7729 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1645   -1.5477    1.0168 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4761    0.2350    1.1314 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8017   -1.3740   -1.4177 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1760   -0.9402   -0.2717 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3838    1.8752   -2.6606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9250    2.4099   -0.8904 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  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 13  1  0
 11 12  2  0
  5 14  1  0
 14 16  1  0
 14 15  2  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  6
  6 26  1  0
  9 27  1  0
  9 28  1  0
 10 29  1  0
 10 30  1  0
 13 31  1  0
 16 32  1  0
M  END


  Mrv0541 02231218592D          

 16 15  0  0  1  0            999 V2000
    0.8047   -0.7744    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8010    0.0532    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0873   -1.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5185   -1.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8047    0.8770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6264   -0.7744    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5185   -2.0120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2359   -0.7744    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0912    1.2907    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5185    1.2907    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3400   -1.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6264    0.8770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0576   -0.7744    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3400    1.2907    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3363    2.1145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0537    0.8731    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  6  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  4  7  1  0  0  0  0
  4  8  2  0  0  0  0
  5  9  1  0  0  0  0
  5 10  2  0  0  0  0
  6 11  1  0  0  0  0
  9 12  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0086726

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCCC[C@H](NC(=O)CCC(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H16N2O5/c10-5-1-2-6(9(15)16)11-7(12)3-4-8(13)14/h6H,1-5,10H2,(H,11,12)(H,13,14)(H,15,16)/t6-/m0/s1

> <INCHI_KEY>
VWXQFHJBQHTHMK-LURJTMIESA-N

> <FORMULA>
C9H16N2O5

> <MOLECULAR_WEIGHT>
232.2337

> <EXACT_MASS>
232.105921632

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
22.765175228727628

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-5-amino-2-(3-carboxypropanamido)pentanoic acid

> <ALOGPS_LOGP>
-3.37

> <JCHEM_LOGP>
-4.065900625952266

> <ALOGPS_LOGS>
-1.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.086430528781067

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3188365035952154

> <JCHEM_PKA_STRONGEST_BASIC>
9.904213305041136

> <JCHEM_POLAR_SURFACE_AREA>
129.72

> <JCHEM_REFRACTIVITY>
53.5456

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.93e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N(2)-succinyl-L-ornithine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0       1.502  -1.446   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.495   0.099   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       0.163  -2.218   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.835  -2.218   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.502   1.637   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.169  -1.446   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.835  -3.756   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.174  -1.446   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.170   2.409   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.835   2.409   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -2.501  -2.218   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.169   1.637   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      -3.841  -1.446   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      -2.501   2.409   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -2.494   3.947   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -3.834   1.630   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6                                                       
CONECT    4    1    7    8                                                  
CONECT    5    2    9   10                                                  
CONECT    6    3   11                                                       
CONECT    7    4                                                            
CONECT    8    4                                                            
CONECT    9    5   12                                                       
CONECT   10    5                                                            
CONECT   11    6   13                                                       
CONECT   12    9   14                                                       
CONECT   13   11                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

View in JSmol

Synonyms

Value	Source
(2S)-5-Amino-2-(3-carboxypropanoylamino)pentanoic acid	ChEBI
(2S)-5-Amino-2-(3-carboxypropanoylamino)pentanoate	Generator
N(2)-Succinylornithine	HMDB

Chemical Formula

C₉H₁₆N₂O₅

Average Mass

232.2337 Da

Monoisotopic Mass

232.10592 Da

IUPAC Name

(2S)-5-amino-2-(3-carboxypropanamido)pentanoic acid

Traditional Name

N(2)-succinyl-L-ornithine

CAS Registry Number

Not Available

SMILES

NCCC[C@H](NC(=O)CCC(O)=O)C(O)=O

InChI Identifier

InChI=1S/C9H16N2O5/c10-5-1-2-6(9(15)16)11-7(12)3-4-8(13)14/h6H,1-5,10H2,(H,11,12)(H,13,14)(H,15,16)/t6-/m0/s1

InChI Key

VWXQFHJBQHTHMK-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, 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
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB
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
Dicarboxylic acid or derivatives
Fatty acid
Amino acid
Carboximidic acid
Carboximidic acid derivative
Carboxylic acid
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Amine
Primary amine
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Primary aliphatic amine
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

N2-acyl-L-ornithine (CHEBI:27574 )

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	-3.4	ALOGPS
logP	-4.1	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	3.32	ChemAxon
pKa (Strongest Basic)	9.9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	129.72 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	53.55 m³·mol⁻¹	ChemAxon
Polarizability	22.77 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