MiMeDB: Showing metabocard for N(5)-[1(S)-1-carboxyethyl]-L-ornithine (MMDBc0056187)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:18:59 UTC

Update Date

2022-08-12 20:09:37 UTC

Metabolite ID

MMDBc0056187

Metabolite Identification

Common Name

N(5)-[1(S)-1-carboxyethyl]-L-ornithine

Description

N(5)-(L-1-carboxyethyl)-L-ornithine, also known as 5-ce-orn, belongs to the class of organic compounds known as alanine and derivatives. Alanine and derivatives are compounds containing alanine or a derivative thereof resulting from reaction of alanine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. Based on a literature review very few articles have been published on N(5)-(L-1-carboxyethyl)-L-ornithine.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222192D          

 16 15  0  0  1  0            999 V2000
    1.0974    2.6664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0461    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3316    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0974    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4750    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8118    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4750    0.6039    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3829    1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5263    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8118    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9039    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8118    2.2539    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4750    2.2539    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  1  0  0  0
  6  3  1  0  0  0  0
  7  5  1  0  0  0  0
  8  6  1  0  0  0  0
  6  9  1  1  0  0  0
 10  4  1  0  0  0  0
 10  5  1  0  0  0  0
 11  7  2  0  0  0  0
 12  7  1  0  0  0  0
 13  8  2  0  0  0  0
 14  8  1  0  0  0  0
  5 15  1  6  0  0  0
  6 16  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0056187

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](N)(CCCN[C@@]([H])(C)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H16N2O4/c1-5(7(11)12)10-4-2-3-6(9)8(13)14/h5-6,10H,2-4,9H2,1H3,(H,11,12)(H,13,14)/t5-,6-/m0/s1

> <INCHI_KEY>
DEGCDQUOHKYOQM-WDSKDSINSA-N

> <FORMULA>
C8H16N2O4

> <MOLECULAR_WEIGHT>
204.226

> <EXACT_MASS>
204.111007003

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
20.89168212015948

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-5-{[(1S)-1-carboxyethyl]amino}pentanoic acid

> <JCHEM_LOGP>
-5.4095931334278

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
2.496499618804805

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.6643258088200268

> <JCHEM_PKA_STRONGEST_BASIC>
10.677864272796743

> <JCHEM_POLAR_SURFACE_AREA>
112.64999999999999

> <JCHEM_REFRACTIVITY>
48.5616

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-amino-5-{[(1S)-1-carboxyethyl]amino}pentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       2.048   4.977   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.953   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.286   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.619   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.048   3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.620   2.667   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.382   2.667   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.954   3.437   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -4.620   1.127   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0       0.715   2.667   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0       4.716   3.437   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       3.382   1.127   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -7.287   2.667   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -5.954   4.977   0.000  0.00  0.00           O+0
HETATM   15  H   UNK     0       3.382   4.207   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0      -4.620   4.207   0.000  0.00  0.00           H+0
CONECT    1    5                                                            
CONECT    2    3    4                                                       
CONECT    3    2    6                                                       
CONECT    4    2   10                                                       
CONECT    5    1    7   10   15                                             
CONECT    6    3    8    9   16                                             
CONECT    7    5   11   12                                                  
CONECT    8    6   13   14                                                  
CONECT    9    6                                                            
CONECT   10    4    5                                                       
CONECT   11    7                                                            
CONECT   12    7                                                            
CONECT   13    8                                                            
CONECT   14    8                                                            
CONECT   15    5                                                            
CONECT   16    6                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

Synonyms

Value	Source
N5-(L-1-Carboxyethyl)-L-ornithine	ChEBI
5-CE-orn	MeSH
N(5)-(1-Carboxyethyl)ornithine	MeSH

Molecular Formula

C₈H₁₆N₂O₄

Average Mass

204.226

Monoisotopic Mass

204.111007003

IUPAC Name

(2S)-2-amino-5-{[(1S)-1-carboxyethyl]amino}pentanoic acid

Traditional Name

(2S)-2-amino-5-{[(1S)-1-carboxyethyl]amino}pentanoic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C8H16N2O4/c1-5(7(11)12)10-4-2-3-6(9)8(13)14/h5-6,10H,2-4,9H2,1H3,(H,11,12)(H,13,14)/t5-,6-/m0/s1

InChI Key

DEGCDQUOHKYOQM-WDSKDSINSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alanine and derivatives. Alanine and derivatives are compounds containing alanine or a derivative thereof resulting from reaction of alanine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alanine and derivatives

Alternative Parents

Substituents

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

non-proteinogenic alpha-amino acid (CHEBI:16770 )
L-ornithine derivative (CHEBI:16770 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-5.4	ChemAxon
pKa (Strongest Acidic)	1.66	ChemAxon
pKa (Strongest Basic)	10.68	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	112.65 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	48.56 m³·mol⁻¹	ChemAxon
Polarizability	20.89 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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_4_2) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-09	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Firmicutes	3	Human ; Human feces

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

113974

KEGG Compound ID

C04210

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

128597

PDB ID

Not Available

ChEBI ID

16770

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for N(5)-[1(S)-1-carboxyethyl]-L-ornithine (MMDBc0056187)

MOL for #<Metabolite:0x00007fecdf758220>

3D MOL for #<Metabolite:0x00007fecdf758220>

3D SDF for #<Metabolite:0x00007fecdf758220>

3D-SDF for #<Metabolite:0x00007fecdf758220>

PDB for #<Metabolite:0x00007fecdf758220>

3D PDB for #<Metabolite:0x00007fecdf758220>

SMILES for #<Metabolite:0x00007fecdf758220>

INCHI for #<Metabolite:0x00007fecdf758220>

Structure for #<Metabolite:0x00007fecdf758220>

3D Structure for #<Metabolite:0x00007fecdf758220>