MiMeDB: Showing metabocard for D-lysopine (MMDBc0055868)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:09:24 UTC

Update Date

2025-10-07 16:09:25 UTC

Metabolite ID

MMDBc0055868

Metabolite Identification

Common Name

D-lysopine

Description

D-lysopine is a plant-derived alkaloid belonging to the class of opines, which are nitrogenous compounds produced by certain plants, particularly in response to Agrobacterium infection. Chemically, D-lysopine is characterized by its unique structure, which includes a lysine moiety linked to a 2-oxoglutarate derivative, contributing to its role in plant metabolism. It is synthesized through pathways involving the conversion of amino acids and organic acids, often in association with other opines such as nopaline and octopine. D-lysopine is involved in the regulation of various metabolic processes, particularly in the context of plant responses to environmental stresses and pathogen interactions. For instance, its production can be stimulated by the presence of certain compounds, as evidenced by the promotion of D-lysopine synthesis alongside other opines in specific experimental conditions (PMID:16657911 ). This highlights its potential role in the intricate signaling pathways that govern plant defense mechanisms and metabolic adaptations.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222092D          

 17 16  0  0  1  0            999 V2000
    6.0474    2.6664    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    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    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
    6.0474    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.7618    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.4763    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    3.0789    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    3.0789    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618    2.2539    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    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  3  1  0  0  0  0
  6  1  1  6  0  0  0
  7  4  1  0  0  0  0
  8  6  1  0  0  0  0
  9  7  1  0  0  0  0
 10  5  1  0  0  0  0
 11  6  1  0  0  0  0
  7 11  1  6  0  0  0
 12  8  2  0  0  0  0
 13  8  1  0  0  0  0
 14  9  2  0  0  0  0
 15  9  1  0  0  0  0
  6 16  1  1  0  0  0
  7 17  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0055868

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H18N2O4/c1-6(8(12)13)11-7(9(14)15)4-2-3-5-10/h6-7,11H,2-5,10H2,1H3,(H,12,13)(H,14,15)/t6-,7+/m1/s1

> <INCHI_KEY>
ZZYYVZYAZCMNPG-RQJHMYQMSA-N

> <FORMULA>
C9H18N2O4

> <MOLECULAR_WEIGHT>
218.253

> <EXACT_MASS>
218.126657068

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
22.704353424149904

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-6-amino-2-{[(1R)-1-carboxyethyl]amino}hexanoic acid

> <JCHEM_LOGP>
-4.9553296820653525

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
3.6143752501757827

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.900443108287919

> <JCHEM_PKA_STRONGEST_BASIC>
10.219223901794843

> <JCHEM_POLAR_SURFACE_AREA>
112.64999999999999

> <JCHEM_REFRACTIVITY>
53.16260000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
lysopine

> <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      11.288   4.977   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.288   3.437   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      12.622   2.667   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.621   4.977   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       1.953   2.667   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       9.955   2.667   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0      13.956   3.437   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      12.622   1.127   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       9.955   5.747   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       7.287   5.747   0.000  0.00  0.00           O+0
HETATM   16  H   UNK     0      12.622   4.207   0.000  0.00  0.00           H+0
HETATM   17  H   UNK     0       7.287   4.207   0.000  0.00  0.00           H+0
CONECT    1    6                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2    7                                                       
CONECT    5    3   10                                                       
CONECT    6    1    8   11   16                                             
CONECT    7    4    9   11   17                                             
CONECT    8    6   12   13                                                  
CONECT    9    7   14   15                                                  
CONECT   10    5                                                            
CONECT   11    6    7                                                       
CONECT   12    8                                                            
CONECT   13    8                                                            
CONECT   14    9                                                            
CONECT   15    9                                                            
CONECT   16    6                                                            
CONECT   17    7                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   32    0
END

Synonyms

Value	Source
(R)-N(2)-(1-Carboxyethyl)-L-lysine	ChEBI
N2-(D-1-Carboxyethyl)-L-lysine	ChEBI
N(2)-(D-1-Carboxyethyl)-L-lysine	ChEBI
Lysopine, (D-lys)-isomer	MeSH

Molecular Formula

C₉H₁₈N₂O₄

Average Mass

218.253

Monoisotopic Mass

218.126657068

IUPAC Name

(2S)-6-amino-2-{[(1R)-1-carboxyethyl]amino}hexanoic acid

Traditional Name

lysopine

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C9H18N2O4/c1-6(8(12)13)11-7(9(14)15)4-2-3-5-10/h6-7,11H,2-5,10H2,1H3,(H,12,13)(H,14,15)/t6-,7+/m1/s1

InChI Key

ZZYYVZYAZCMNPG-RQJHMYQMSA-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
D-alpha-amino acid
Medium-chain fatty acid
Amino fatty acid
Dicarboxylic acid or derivatives
Fatty acid
Fatty acyl
Amino acid
Carboxylic acid
Secondary aliphatic amine
Secondary amine
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Organopnictogen compound
Organic nitrogen compound
Carbonyl group
Organic oxygen compound
Amine
Organic oxide
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

L-lysine derivative (CHEBI:17213 )
amino acid opine (CHEBI:17213 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-5	ChemAxon
pKa (Strongest Acidic)	2.9	ChemAxon
pKa (Strongest Basic)	10.22	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	8	ChemAxon
Refractivity	53.16 m³·mol⁻¹	ChemAxon
Polarizability	22.7 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_2_1) - 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

Microbial Pathways

Pathways

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank	Species

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated 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/Eubacteria	Proteobacteria	3

Exposure Sources

Other Exposures

Source Type	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

C00001544

Chemspider ID

167647

KEGG Compound ID

C04020

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

193187

PDB ID

Not Available

ChEBI ID

17213

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 D-lysopine (MMDBc0055868)

MOL for #<Metabolite:0x00007f2ad7486ad0>

3D MOL for #<Metabolite:0x00007f2ad7486ad0>

3D SDF for #<Metabolite:0x00007f2ad7486ad0>

3D-SDF for #<Metabolite:0x00007f2ad7486ad0>

PDB for #<Metabolite:0x00007f2ad7486ad0>

3D PDB for #<Metabolite:0x00007f2ad7486ad0>

SMILES for #<Metabolite:0x00007f2ad7486ad0>

INCHI for #<Metabolite:0x00007f2ad7486ad0>

Structure for #<Metabolite:0x00007f2ad7486ad0>

3D Structure for #<Metabolite:0x00007f2ad7486ad0>