MiMeDB: Showing metabocard for D-octopine (MMDBc0055871)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:09:29 UTC

Update Date

2022-08-12 20:09:28 UTC

Metabolite ID

MMDBc0055871

Metabolite Identification

Common Name

D-octopine

Description

Octopine belongs to the class of organic compounds known as arginine and derivatives. Arginine and derivatives are compounds containing arginine or a derivative thereof resulting from reaction of arginine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. Octopine is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on Octopine.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222092D          

 19 18  0  0  1  0            999 V2000
   -0.5230   -1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3349   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6204   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0493   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230   -1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9059   -1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059   -1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4783   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1927   -1.1270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4783    0.1105    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7638   -1.1270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914   -0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9520   -1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375    0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914   -2.3645    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6204   -2.3645    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -1.5395    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6204   -1.5395    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  6  0  0  0
  6  3  1  0  0  0  0
  7  5  1  0  0  0  0
  8  6  1  0  0  0  0
 10  9  2  0  0  0  0
 11  9  1  0  0  0  0
 12  4  1  0  0  0  0
 12  9  1  0  0  0  0
 13  5  1  0  0  0  0
  6 13  1  6  0  0  0
 14  7  2  0  0  0  0
 15  7  1  0  0  0  0
 16  8  2  0  0  0  0
 17  8  1  0  0  0  0
  5 18  1  1  0  0  0
  6 19  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0055871

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H18N4O4/c1-5(7(14)15)13-6(8(16)17)3-2-4-12-9(10)11/h5-6,13H,2-4H2,1H3,(H,14,15)(H,16,17)(H4,10,11,12)/t5-,6+/m1/s1

> <INCHI_KEY>
IMXSCCDUAFEIOE-RITPCOANSA-N

> <FORMULA>
C9H18N4O4

> <MOLECULAR_WEIGHT>
246.267

> <EXACT_MASS>
246.132805076

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
24.288603415695604

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-5.109541236794499

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
3.3953998769065152

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.675843111964066

> <JCHEM_PKA_STRONGEST_BASIC>
12.150235385792655

> <JCHEM_POLAR_SURFACE_AREA>
148.53

> <JCHEM_REFRACTIVITY>
69.27619999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
octopine

> <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      -0.976  -3.644   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.358  -2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.025  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.692  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.976  -2.104   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.691  -2.104   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.691  -3.644   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.359  -1.334   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       9.693  -2.104   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       8.359   0.206   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       7.026  -2.104   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       0.357  -1.334   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0      -3.644  -2.104   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -2.310   0.206   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.357  -4.414   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       3.025  -4.414   0.000  0.00  0.00           O+0
HETATM   18  H   UNK     0      -2.310  -2.874   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       3.025  -2.874   0.000  0.00  0.00           H+0
CONECT    1    5                                                            
CONECT    2    3    4                                                       
CONECT    3    2    6                                                       
CONECT    4    2   12                                                       
CONECT    5    1    7   13   18                                             
CONECT    6    3    8   13   19                                             
CONECT    7    5   14   15                                                  
CONECT    8    6   16   17                                                  
CONECT    9   10   11   12                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    4    9                                                       
CONECT   13    5    6                                                       
CONECT   14    7                                                            
CONECT   15    7                                                            
CONECT   16    8                                                            
CONECT   17    8                                                            
CONECT   18    5                                                            
CONECT   19    6                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   36    0
END

Synonyms

Value	Source
D-(+)-Octopine	ChEBI
N2-(1-Carboxyethyl)-L-arginine	ChEBI
N2-(D-1-Carboxyethyl)-L-arginine	ChEBI
N(2)-(D-1-Carboxyethyl)-L-arginine	ChEBI
N'-(1-carboxyethyl)arginine	MeSH
N2-(Carboxyethyl)-L-arginine	MeSH

Molecular Formula

C₉H₁₈N₄O₄

Average Mass

246.267

Monoisotopic Mass

246.132805076

IUPAC Name

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

Traditional Name

octopine

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C9H18N4O4/c1-5(7(14)15)13-6(8(16)17)3-2-4-12-9(10)11/h5-6,13H,2-4H2,1H3,(H,14,15)(H,16,17)(H4,10,11,12)/t5-,6+/m1/s1

InChI Key

IMXSCCDUAFEIOE-RITPCOANSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as arginine and derivatives. Arginine and derivatives are compounds containing arginine or a derivative thereof resulting from reaction of arginine 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

Arginine and derivatives

Alternative Parents

Substituents

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

guanidines (CHEBI:15805 )
secondary amino compound (CHEBI:15805 )
amino dicarboxylic acid (CHEBI:15805 )
amino acid opine (CHEBI:15805 )
D-arginine derivative (CHEBI:15805 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-5.1	ChemAxon
pKa (Strongest Acidic)	2.68	ChemAxon
pKa (Strongest Basic)	12.15	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	148.53 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	69.28 m³·mol⁻¹	ChemAxon
Polarizability	24.29 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

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/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

C00001549

Chemspider ID

97253

KEGG Compound ID

Not Available

BioCyc ID

CPD-309

BiGG ID

Not Available

Wikipedia Link

Octopine

METLIN ID

Not Available

PubChem Compound

108172

PDB ID

Not Available

ChEBI ID

15805

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 D-octopine (MMDBc0055871)

MOL for #<Metabolite:0x00007f9206381f18>

3D MOL for #<Metabolite:0x00007f9206381f18>

3D SDF for #<Metabolite:0x00007f9206381f18>

3D-SDF for #<Metabolite:0x00007f9206381f18>

PDB for #<Metabolite:0x00007f9206381f18>

3D PDB for #<Metabolite:0x00007f9206381f18>

SMILES for #<Metabolite:0x00007f9206381f18>

INCHI for #<Metabolite:0x00007f9206381f18>

Structure for #<Metabolite:0x00007f9206381f18>

3D Structure for #<Metabolite:0x00007f9206381f18>